Here are some commercials that aired during The Wonderful World of Disney presentation of Atlantis- The Lost Empire:

1. RadioShack
2. Harry Potter and The Chamber of Secrets on DVD & Video
3. Visa Check Card
4. Applebee's
5. PediaSure
6. Hershey's Chocolate Bar
7. 'The Wonderful World of Disney' will continue in a moment
8. 8 Simple Rules for Dating my Teenage Daughter/According to Jim/Lost At Home ABC promos
9. Entertainment Tonight ABC 6 promo
10. ShelterGuard Systems
11. Scioto Valley
12. Farm Rich Pizzatas
13. NewsCenter on ABC 6 Weather promo
14. We now return to 'The Wonderful World of Disney'
15. Old Navy
16. Lubriderm Skin Therapy Lotion
17. Diet Pepsi
18. Jimmy Dean Fast Breakfasts
19. Oust Air Freshener Spray
20. M&Ms
21. Hotels.com
22. My Wife & Kids & George Lopez ABC promos
23. ABC ID (2003)
24. (same as #14)
25. Michael Eisner Intershow
26. You're watching 'The Wonderful World of Disney' here on ABC!
27. Toys R' Us
28. Quaker Quakes Corn Rings
29. Mazda 6i
30. Wendy's Garden Sensations Salads
31. Almay Bright Eyes Mascara
32. Swanson Dinners
33. Pirates of The Carribean: The Curse of The Black Pearl trailer
34. Kim Possible promo
35. Regular Joe ABC promo
36. Coming up Tonight on NewsCenter at 11:00pm...
37. Burger King
38. Chris' Garden on NewsCenter promo
39. Ohio Tobbaco Use Prevention & Control Foundation
40. Chris Bradley NewsCenter promo
41. Who Wants to Be A Millionaire? ABC 6 promo bumper
42. (same as #14)
43. Dr. Dolittle ABC promo
44. Ford Motor Company (100 Years)
45. Florida Orange Juice
46. MCI
47. Cingular Wireless
48. KFC Honey BBQ Boneless Wings
49. FannieMae Foundation
50. Energizer Max Batteries
51. Crest Whitening Plus Scope Toothpaste
52. (same as #8, #14 & #17)
53. The UPS Store
54. Red Lobster
55. Maybelline EverFresh Makeup
56. Bissell Cleanview Vacuum
57. Band-Aid Liquid Bandages
58. Wal-Mart
59. Allstate Insurance
60. According to Jim & Lost At Home ABC promos
61. Split-Screen Credits (Alias/Dragnet/America's Funniest Home Videos/8 Simple Rules for Dating my Teenage Daughter/Lost At Home/Eloise at the Plaza promos)
62. Massey's Pizza

Video footage courtesy of Justin-Smith (loveforlogos2) at archive.org
All credit of this footage goes to him.