Below details first on the draw and then on the group matches

The Draw

A drastic 'punishment' for Côte d'Ivoire has been the result of the draw of the qualifyers for the 2004 Nations Cup which was held Jan 8 at Bamako, Mali. 
Not only will they have to play South Africa to be at Tunisia 2004, they will have to finsih first in the group as this is one of the groups where the second will have no chance.
Explaination:

The scheme for qualification has been modified so that the samller teams have more matches. There will be no preliminary knock out round. Instead there are 13 groups from which 10 contain four teams, the remaining 3 groups contain three teams each.
Qualified for the 2004 Nations Cup will be Tunisia (hosts), the title holders (Cameroon), and the winners of 13 qualifying groups. Plus the best runners up of those 10 groups which contain 4 teams. 

Because the seeding and draw had been made top down (alternative: bottom up) the three groups with three teams are not any easier, they just do not contain a clear outsider.
The group 11 with South Africa, Côte d'Ivoire, and Burundi (who are at least a factor at home) is by far the heaviest and allows no team to sneak in as group second.
The decision why Côte d'ivoire was seeded as the only team of the 2002 Nations Cup into the second pot although they almost qualified for the World Cup and are regulars at almost all Nations Cup finals where they have won the edition 1992, finished third 1994, remained unexplained. Speculating, the only possible explaination seems to be that simply a virtual 2002 tournament table, where they finished last, has been the sole criteria.

The other groups seem better balanced, most of them with a favorite (one of the 2002 participiants), a most likely challenger plus outsider(s). Promising races contain Nigeria-Angola (Group 1), Guinea-Liberia (Group 2), Zambia-Sudan (Group 3), Burkina Faso-Congo (Group 4), Mali-Zimbabwe (Group 6), or DR Congo-Libya (Group 9). Compared to Group 11 the most lightweighted group seems Group 5 where Kenya will still have a hard time to  break the East African jinx this time against group heads Togo.
In Group 8 a curiousity attracting match up will pitch the 2002 runners up against the recently promising lightweights Lesotho and Gambia, which should be a just too high mountain to climb for the two.

official data as published by CAF Online:

The draw of the 2004 African Cup of Nations tournament was held on 8^th January in Bamako.
49 countries have sent their engagements to participate in the preliminary qualifying tournament 
The participating countries were divided into 10 groups of 4 and 3 groups of 3.
The first teams of each group will directly qualify for the final tournament in addition to the best second of the groups formed of 4 teams
First seeded teams
Senegal, Mali, Nigeria ,Egypt, South Africa, RD Congo, Ghana, Liberia, Morocco, Togo, Zambia, Burkina Faso, Algeria.
Second seeded 
Cote d’Ivoire, Angola, Madagascar, Congo, Gabon, Ouganda, Lesotho, Libya, Kenya, Zimbabwe, Namibia, Sudan, Guinea.
Third seeded 
Burundi, Mauritius, Malawi, Chad, Ethiopia, Eritrea, Sierra Leone, Gambia, Mozambique, Tanzania, Swaziland, Cap Verde, Rwanda.
Fourth seeded
Benin, Botswana, Djibouti, Equatorial Guinea, Guinea Bissau , Mauritania, Niger, 
Centrafrique, Sao Tome, Seychelles.

The draw gave the following groups 
Group 1: Angola, Djibouti (withdrawn), Malawi, Nigeria
Group 2: Ethiopia, Guinea, Liberia, Niger
Group 3: Benin, Sudan, Tanzania, Zambia 
Group 4: Burkina Faso, Central African Republic, Congo, Mozambique
Group 5: Cape Verde Islands, Kenya, Mauritania, Togo
Group 6: Eritrea, Mali, Seychelles, Zimbabwe
Group 7: Equatorial Guinea, Gabon, Morocco, Sierra Leone
Group 8: Gambia, Lesotho, Sao Tome and Principe (withdrawn), Senegal
Group 9: Botswana, DR Congo, Libya, Swaziland
Group 10: Egypt, Guinea Bissau (withdrawn), Madagascar, Mauritius
Group 11: Burundi, Ivory Coast, South Africa
Group 12: Algeria, Chad, Namibia
Group 13: Ghana, Rwanda, Uganda

Best second in the groups of 4 to be determined according to : 
1. Higher number of points
2. Better goal difference
3. Higher number of goals scored
4. play-off game
 

African Nations Cup Qualifiers: the matches

Group 1
in italics: preview before the match

Angola - Nigeria  0:0
Important predeciding match:
Angola, full of young talent, are the main challengers for Nigeria. Nigeria still with problems, another new coach, whose appointment is already criticised, and a lot of players who have excused themselves because of injury.
Angola will need to win if they want to make it a real race as they have been much weaker in away games in recent competitions.

Malawi - Angola  1:0
Malawi clinched a victory in their first group 1 match over the ambitious and hopeful Angolans who are now far away from being able to challenge group favorite Nigeria. Teenage striker Mwafulirwa scored with only few minutes to go when Angola were aiming for their second successive scoreless draw

Malawi-Nigeria  0:1
goal: John Utaka, '10
Jay Jay Okocha led NIgeria to a vital coup against a sometimes dangerous home side

Nigeria - Malawi  4:1
An early lead by Malawi, but it did not take long before the match was decided 3:1 in favour of the Nigerians who added a fourth goal in second half. Two goals by the great talent Ayiegbeni who had already impressed in European Cup for his then Israeli side and is now playing for Portsmouth, who became promoted to the Premier League.

Important predeciding match:
Guinea - Liberia  3:0 
Important predeciding match:
Game 1 after George Weah for Liberia and Guinea, once more successful as their fellow West Africans, see the chance to return to the African Nations Cup finals after the FIFA ban. They need to win.
Niger - Ethiopia   3:1
Interesting match:
the two group outsiders: Niger a poor country and probably without chance to ualify, but Ethiopia as a slim chance to enter the race. Provided they steal those three points

Ethiopia - Guinea  1:0
Liberia - Niger 1:0

Ethiopia - Liberia  1:0
Guinea - Niger 2:0
goals: Yansare Fode '40, Abdoulaye Sylla '89

Niger - Guinea  1:0
Shock defeat for Guinea who seem to waste their good opportunity to return to the big stage by poor away results. Niger now with the same chances as all matches in this group so far have produced home wins.
Liberia - Ethiopia  1:0

Important predeciding match:
Sudan - Zambia   0:1
Sudan see the chance to snap away Zambias place at the finals as the Zambians continue to have administrative and financial problems. So they could not persuade their German professionals to play. Sudan need to win, other results will put Zambia in a comfortable position.
1st half: a match of two teams with limited tools on a bumpy ground which made a more enetertaining match impossible. Zambia looking more sharp and their defensive play beginning at the midfield line was interrupting the Sudanese build up quite effectively.
-('6) Zambia free kick against goalpost
2nd half: a much more determined Sudanese side with more movement, aggresiveness and some more long crosses, suitable for the pitch. Zambia pinned back into defence with a late surprise for the hosts: Suddenly spotting the opportunity in the 90th minute they had the defenders outnumbered and scored the vital decxiding goal.
Benin - Tanzania  4:0
Interesting match:
the two group outsiders: The winner could stay in the race for some time at least mathematically. Both are basically talented but lack professionalism, Benin are from West Africa and should be talented like their neighbours, Tanzania one of the more populated countries but from the weak East African region.

Tanzania - Sudan  1:2
Tanzania slumped again and are almost already out of the race while Sudan successfully bounced back from home defeat to Zambia and cannot be counted out yet. After an early lead for the home team Machupa ('20), the Sudanese came back quickly ('29) and decided the match early into second half by a penalty.
Zambia - Benin  1:1
Disappointment for the Zambians, who again had a chaotic build up to the match and this time had to pay the bill. Benin took the lead (Oladipipo) before crowd trouble seemed to have marred the match (as usual when a home team loses). Zambia equalised through Kilambe midway second half

Sudan - Benin  3:0
Tanzania-Zambia  0:1 
goal: Lungu '27
Zambia back in promising position after the second success on the road.

Benin - Sudan  3:0
Zambia - Tanzania 2:0
Two goals by Harry Milanzi have brought Zambia close to qualification for Tunisia 2004 against tired visitors who had travelled 36 hours on the road

C.A.R. - Mozambique 1:1
the two group 4 outsiders and a rare home match for the poor Central African republic.
Congo (Brazzaville) - Burkina Faso  0:0  (final score, Guie-Mien missed penalty)
Important predeciding match:
Congo are main challengers for the West African favorites and need to win to make it a race.
They will play with their star player Rolf Christel Guie Mien from German 2nd Bundesliga club Eintracht Frankfurt

Burkina Faso - Central African Republic  2:1
Although being reported tired from a stressing trip, the visitors took the lead after 38 minutes through a Dehande header. Burkina Faso, who had hit the framework twice, equalised after 60 minutes (Amadou Toure free kick) and got the winner 15 minutes later (Minoungou). 
Mozambique v Congo  0:3
Three second half goals, including a free kick by Rolf Christel Guie-Mien provided an impressive Congolese answer to their first match disappointment. 

Mozambique - Burkina Faso  0:0
goal: Monteiro Dario 89
Congo - C.A.R. 2:1
Congo: Embingou Rock Sihplice 7, Ewolo Oscar Tony 53, CAR: Igor Habita 85

Burkina Faso - Mozambique  4:0
Dagano ('6),('8), Amadou Touré ('34), Minoungou ('87)
CAR - Congo  0:0
 

Kenya - Togo   3:0
Important predeciding match:
Kenya want to return after a long time of absence of East African football. Herefore they need to take Togos place at the finals. Winning this match seems to be vital for the plan.
Mauretania - Cape Verde  0:2
two real outsiders

Cape Verde - Kenya   0:1
Braza ('58). sent off: Opiyo (Kenya, '80)
Togo - Mauritania  1:0
Adabyo scored and Togo secured 3 points while wasting a penalty. An unconvincing result but enough to secure indispensable 3 points to remain in the race

Cape Verde - Togo  2:1
The second shock for the Togolese who might face abscence from  Nations Cup after three successive qualifications
Kenya - Mauretania  4:0
Kenya made no mistakes and are now heavy favorites to lift the jinx on East African football and bring it back to the Nations Cup for the first time since 1992

Togo - Cape Verde 5:2 
Mauretania - Kenya 0:0
 

Seychelles - Eritrea  1:0  (Victor '50, att. 3,000)
Interesting match as outsiders Eritrea could boost their hopes, provided they take all three here.
Zimbabwe - Mali  1:0
Important predeciding match:
Zimbabwe, often on the verge of qualification with another attempt to qualify. Mali want to make a big step right in the first match.

Eritrea - Zimbabwe  0:1
Peter Ndlovu scored after 6 minutes and Zimbabwe survived a late scare on a bumpy pitch to walk away with 3 very important away points to confirm their bid to reach the Nations Cup finals a first time 
Mali - Seychelles  3:0
Goals by Seydou Keita, debutant Mamady Sidibe, and Dramane Coulibaly secured the expected 3 points for Mali who are under heavy pressure in this group after surrendering the first match to Zimbabwe.

Zimbabwe - Seychelles  3:1
Zimbabwe with more problems than expected to break down the resistance of the outsiders
Eritrea - Mali  0:2
Very important away win for Mali who are pursuing the yet perfect Zimbabweans and must stay within 3 points to keep their chances before the return match between the group's giants

Seychelles - Zimbabwe 2:1
Zimbabwe payed the price for arriving with a squad that missed key players. A penalty ('75) and after the meanwhile equalizer, a free kick few minutes before the end of the match sealed the victory for the outsiders.
Mali - Eritrea  1:0
 

Gabon - Morocco  0:1   (Chippo '16)
Morocco, traditionally with some problems against African opponents in a group difficult to predict. Gabon and Sierra Leone are very inconstant in their performance but if one of the two emerges as opponent, it could become uncomfortable for the North Africans. Gabon usually difficult to play against at their turf.

Equ. Guinea - Sierra Leone 1:3?
Sierra Leone with the attempt to return to the Nations cup need to take the three points. then they might have a chance.
Morocco - Equatorial Guinea  5:0
Sierra Leone - Gabon  2:0

Gabon - Equ. Guinea  4:0
Sierra Leone - Morocco  0:0
Sierra Leone were dominating the match but could not get the ball into the goal, great saves by the Moroccan keeper. The North Africans now in the best position.

Equ. Guinea - Gabon  2:1
Morocco - Sierra Leone  1:0
Morocco seem to have switched from Puma to Nike and play in green.
The first 25 minutes see a defensive struggle for Sierra Leone as the pressure of the hosts keeps the ball in the half of the visitors. The sheer number of penalty area situations make it logical that Morocco scores: one of the inumerous defended balls flies to the feet of Chippo who fires the ball past the keeper with a bouncing volley from about 20 meters after 25 minutes.
Morocco continue to dominate but as the half reaches the end, loses grip a little.
1715 GMT: 2nd half starts. Sierra Leone have to attack now and they try. But their passing game (which is not helped by the pitch) is far from being fluent and so many attacks are interrupted before producing dangerous situation. Morocco themselves look far less convincing than in the first 30 minutes as not losing the advantage seems predominant in their minds rather than goal hunger. Their bggest goal scene comes after 84 minutes when the Sierra Leone keeper masterly saves what would have been an own goal by one of his defenders.
Although Sierra Leone hurry they are incapable to impose a real pressure on the hosts due to their fragmented style even though their star player Mohammed Kallon is working a lot for it.

Morocco - Gabon  2:0
1:0 ('24) #11 header
2:0 ('75) #7, a fine solo by one of the more conspicious players
A Moroccan team that seems to be a few miles away from the class of the battles with Senegal and egypt for the World Cup qualification 2002 and even further from the flamboyance of 1998.
Still with enough quality to beat Gabon clearly.
Speaking of flamboyance it was the Gabonese players who displayed a lust in treating the ball with style that seems to have gone lost in some African games. A great display of talent by the seemingly young players, but in the same time inexperienced and error ridden, still easily contained by the Moroccan defence.
Morocco has not conceded a goal yet.

Lesotho - Senegal  0:1
Interesting match:
game 1 for Senegal after the Metsu era. Senegal without El Hadji Diouf and Salif Diao from Liverpool.
Lesotho had been the surprise package of the 2002 qualifiers but had lacked stamina in the end.

Gambia - Lesotho  6:0

Gambia - Senegal  0:0
Gambia surprised in the first half and had several chances to score. In the second half Senegal were able to gain more control on the match but without scoring.

Senegal - Lesotho 3:0
Senegal qualify for Tunisia 2004, goals: Diouf (pen.), H.Camera
 

Botswana - Swaziland   0:0
interesting match between the two minnows. But do not underestimate anybody, Swaziland has already staged a few surprisess in single matches.
Libya - DR Congo 3:2
The two favorites of group 9 - Ambitious Libya, probably much better prepared, will seek to bag the three points they need. The Congolese, full of talent but with many organisational problems, could take away momentum from the North Africans by stealing a point or more. 
1st half: A thrilling match and some good football, especially the fast passing game of the Libyans.
Great goal after about 15 minutes when a through ball between the defenders beat the Congolese and the hosts scored. DR Congo answered with a goal, a header by Nonda 10 minutes later against a respectful and nervous Libyan defence.
After some missed chances, Libyan Nummer 7's header was the final point and #14's through ball had been the initial of a fantastic combination that took the Congolese defense apart and provided the next Libyan goal.
Then #14's flamboyant trickery also forced a foul inside the penalty area only two minutes later, the kick was converted by #3?.
A dangerous Congolese freekick was saved only a minute later.
2nd half: Congo came out of halftime determined and with only few minutes played #11 beat the Libyan keeper with an impressive 25 meter shot into the corner. 
Libya found back into the match and after promising chances on both sides it were the inspired Libyans who should have scored more.
The Libyan defence remained nervous against the more agressive Lualua & Co. still but survived a last late pressure period.
A great game for the North Africans coached by former Tunisian coach Scolgio from Italy.
The Congolese did not really play bad but lost too many balls against an opponent specialised in fast clear drawn (counter) attacks into offered spaces.

DR Congo - Botswana  2:0
highlights: 1:0 ('5) Lualua 2:0 ('21) Mpuana, Nonda free kick against the bar and Lualua 2nd yellow card sent off, att. 60,000
Swaziland - Libya  2:1
Libya had taken the lead through a first half penalty but the hosts surprised the North Africans with a comeback within the last 10 minutes.

Swaziland - DR Congo  1:1
After having beaten Libya last October, Swaziland, the groups surprise package now went after the Congolese and took an early lead (Dlamini) before a second half goal by Musara put the Congolese into the now relatively best position in the group. One thing seems sure: the group second will hardly have enough points to become the backdoor qualificant for the finals.
Libya-Botswana  0:0
Since the (forced) departure of coach Scolgio Libya seem to be unable to keep up their sometimes surprising form

Botswana - Libya  0:1
A late goal saved Libya's chances in what was reported a dull game
DR Congo - Swaziland  2:0

Madagascar - Egypt 1:0 (final score)
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Egypt, with new coach Saleh from surprise champions Ismailia, clear favorites in this group. Madagascar and Mauritius, quite strong at home but much weaker away, might stage a surprise in a single game but qualifying would be a real sensation.

Mauritius - Madagascar  0:1
Madagascar makes this group thrilling - at least on paper. A first half goal ensured maximum 6 points for the guests and sets up a more than though difficult catch up race for the trailing Egyptians.

Mauritius - Egypt  0:1 
goal: Mido, 1st half

Egypt - Mauritius  7:0
In Egypt and Côte d'Ivoire the hunt for goal difference might become crucial. A problem is the 3 team format of the groups. In the last match both teams might have to watch nailbiting while their competitors for the first place, Madagascar and South Africa, will have the advantage of playing the same opponents as the two today, but knowing the scoreline they might need. This all of course is a bit premature because the teams (Egypt - Madagascar, South Africa - Côte d'Ivoire) will face each other first directly in two weeks time and those two matches do not necessarily end with the expected results.
Egypt with very high tempo from beginning to end and good combinations against pathetic defending scored and scored and still wasted a good number of quality chances

Egypt - Madagascar  6:0
A brilliant early ('2 Tabey) 30 meter free kick strike strike reliefed the hosts and frustrated the visitors who would have qualified for the Nations Cup finals in case of a draw. The Egyptians, let loose, like two weeks ago, did not want to make any mistakes and took apart the islanders by their in such cases of confidence fluently executed ambitious game comprising all features of attacking football, i.e. a well developed passing game. 
This produced a typical attack using the left wing, and a perfect cross and header for a schoolbook type second goal ('10 Bilal). The third ('25 Bilal) was rather due to an odd looking defense after a corner and the fourth a deflected free kick ('42 Mido)
In the second half Egypt did not relief the grip on the disillusioned visitors and Bilal intentionally deflected a Mido shot into the net for the 5th after 58 minutes.
A counter saw Mido set up Ahmed Bilal for the sixth goal then ('86).
Seconds later Madagascar missed the chance of putting one back when they blew the ball across the bar after a very well performed combination.
It has to be mentioned that every goal has been important: In theory Madagascar can still qualify instead of Egypt whatever the scoreline is today. But they will need to beat Mauritus by double the scoreline of today plus 5 goals. So for every Egyptian goal today they will have to shoot two more in their last match against Mauritius at Madagascar in two weeks (17-0 now).

Côte d'Ivoire - South Africa  0:0 
Important predeciding match:
clash of the titans and a must win situation for the home team.
In groups of three there are only two home games...

South Africa - Burundi  2:0

Burundi - Côte d'Ivoire  0:1
A Bakari goal secured three points for the Elephants who are in a tough race with South Africa for a place at Tunisia. After yearlong back-and-fourth decisions Bakari, who was raised and plays at France had finally agreed to make his debut for the West Africans.

Côte d'Ivoire - Burundi  6:1
In Egypt and Côte d'Ivoire the hunt for goal difference might become crucial. A problem is the 3 team format of the groups. In the last match both teams might have to watch nailbiting while their competitors for the first place, Madagascar and South Africa, will have the advantage of playing the same opponents as the two today, but knowing the scoreline they might need. This all of course is a bit premature because the teams (Egypt - Madagascar, South Africa - Côte d'Ivoire) will face each other first directly in two weeks time and those two matches do not necessarily end with the expected results.
Drogba with a first half hattrick, his replacement Bakari adds two more after halftime, Dindane the sixth, before Burundi scores
 

Namibia - Algeria  0:1
dzfoot reports: own goal by Benjamin Collins ('4) (Collin Benjamin?)
Algeria: Gaouaoui - Haddou (C.), Raho - Boudjakdji, Zafour, Driouèche - Belkaïd, Kraouche, Mezghiche - Daoud B., Akrour  (coach Hamid Zouba)
important predeciding match:
Namibia, recently weak in away games, will need to win if they really want to challenge the favorite North Africans.

Algeria - Chad 4:1
att. 20 000 
goals: Akrour ('26, '72), Belmadi ('54, '69) for Algeria, Naâma Naay ('70) Chad
sent off: Raho ('25) (Algeria)
Algeria: Gaouaoui - Raho, Haddou (c.), Drioueche, Zafour - Belkaïd, Mansouri, Kraouche (Abaci, 83e) - Belmadi, Akrour (Daoud B., 88e), Amaouche Y. (Ghazi K., 46e).
bench : Samadi, Mezghiche, Arribi, Bendahmane, coach: Hamid Zouba
Chad : Teinder, M'Baïmdja, Nandé, Oumar, Djiddo, Nodji, Djeradbi, M'baye, Jeffise (Naama Naay 35e), Kalo Waye (Mohamed Ahmed 55e), Baba Mohamed (cap), Banayiye, Giedji
bench: Gueadji, Molingar, Otombaye, Abdoulaye, coach: Jean Paul Akono
best player: Belmadi
(thanks to Francisco sending the dzfoot.com report)

Chad - Namibia 2:0

Namibia - Chad  2:1
Namibia needed a penalty to decide the match with a quarter to go

Algeria - Namibia  1:0
Not very convincing but succesful in the end, Algeria qualified for the Nations Cup through a first half goal

Uganda - Ghana 1:0    (Obwiny '52)
Important predeciding match:
Uganda are the main challengers for Ghana in group 13 and winning points in this away match would already be a big step for the West Africans. Ghana have a new coach once more, who seems to have dropped the ideas of his predecessors and has recalled many established Euoropean based professionals with the exception of Samuel Kuffour.

Ghana - Rwanda  4:2
After a 2:2 halftime score, Ghana managed to escape another embarrassment thanks to second half goals by Charles Taylor and Derek Boateng

Rwanda - Uganda  0:0

Uganda - Rwanda  0:1
A grotesk incident, involving the guests keeper and black magic allegations, was initial point to a hot headed fight and an ill tempered game which the outsiders surprisingly won through a first half goal.
The result lifts a bit of pressure on Ghana who had lost in Uganda and were idle this weekend