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These are the Top 100 Greatest Cartoons according to Wizard Magazine (issue #121). For a list of TV shows, it definitely shows Wizard's comic book predilection. This list was transcribed by Jon "WB" Gray. Thanks Dub!

100. M.A.S.K.
99. She-Ra
98. The Yogi Bear Show
97. Transformers: Beast Machines
96. Josie and the Pussycats
95. SilverHawks
94. Voltron: Defender of the Near Universe
93. Jem
92. Where on Earth is Carmen Sandiego?
91. Cow & Chicken
90. Neon Genesis Evangelion
89. Sailor Moon
88. Static Shock
87. Aladdin: TV Series
86. Daria
85. Inspector Gadget
84. Spider-Man: 60's version
83. Marvel Superheroes
82. The Woody Woodpecker Show
81. The Inhumanoids
80. Transformers: Beast Wars
79. Popeye
78. Jayce and the Wheeled Warriors
77. Histeria!
76. Invader ZIM
75. Saturday Night Live: TV Funhouse
74. The Zeta Project
73. Men in Black
72. The Maxx
71. The Jetsons
70. Speed Racer
69. The Bullwinkle Show
68. Johnny Bravo
67. Mighty Mouse Playhouse
66. Aeon Flux
65. Tiny Toon Adventures
64. Muppet Babies
63. Challenge of the Superfriends
62. Danger Mouse
61. King of the Hill
60. Beavis & Butt-Head
59. Smurfs
58. Teenage Mutant Ninja Turtles
57. The Critic
56. The Flintstones
55. Darkwing Duck
54. Scooby's All-Star Laff-A-Lympics
53. He-Man and the Masters of the Universe
52. Clerks
51. Thundercats
50. Dragon Ball Z
49. X-Men: Evolution
48. Spawn
47. Thundarr the Barbarian
46. Defenders of the Earth
45. The Herculoids
44. Freakazoid!
43. Space Ghost
42. X-Men
41. Dungeons & Dragons
40. Dr Katz, Professional Therapist
39. Scooby-Doo
38. The Adventures of the Galaxy Rangers
37. Spider-Man and His Amazing Friends (80's)
36. The Real Ghostbusters
35. Rugrats
34. Mobile Suit Gundam Wing
33. Robotech
32. Family Guy
31. Star Blazers
30. Voltron: Defender of the Universe
29. Gargoyles
28. Spider-Man: The Animated Series - 90's version....
27. Futurama
26. DuckTales
25. Fantastic Four
24. Schoolhouse Rock
23. Animaniacs
22. Peanuts/The Charlie Brown And Snoopy Show
21. Superman: The Animated Series
20. SpongeBob SquarePants
19. Fat Albert and the Cosby Kids
18. Pinky and The Brain
17. South Park
16. The Tick
15. Tom and Jerry
14. The Tex Avery Show
13. Dexter's Laboratory
12. Ren & Stimpy
11. Space Ghost Coast to Coast
10. The Powerpuff Girls
9. Battle of the Planets
8. Jonny Quest
7. G.I. Joe: A Real American Hero
6. Batman Beyond
5. Transformers
4. Superman: Max Fliescher Version
3. The Bugs Bunny Show/Looney Tunes
2. Batman: The Animated Series
1. The Simpsons

TV Guide picked the 50 greatest cartoon characters of all time in the issue for August 3rd, 2002. It's still just as controversial as Wizard's but at least they included the most underrated cartoon character ever at number 18. Here is the list, transcribed by Jerry Beck and Cartoon Research:

50. Tom and Jerry
49. Speed Racer
48. Bobby Hill from King of the Hill
47. Porky Pig
46. Woody Woodpecker
45. Boris Badenov and Natasha Fatale
44. Alvin (The Chipmunk)
43. Donald Duck
42. Wonder Woman
41. Daria
40. Batman
39. Superman
38. Wile E. Coyote and Road Runner
37. Mighty Mouse
36. Yogi Bear and Boo Boo
35. Space Ghost
34. Bill from Schoolhouse Rock
33. Tweety and Sylvester
32. Tom Terrific
31. Ren and Stimpy
30. George of the Jungle
29. Mr. Magoo
28. Felix The Cat
27. Winnie the Pooh
26. Arthur
25. Heckle and Jeckle
24. Josie and the Pussycats
23. Underdog
22. Scooby-Doo
21. Gerald McBoing-Boing
20. Popeye
19. Mickey Mouse
18. Top Cat
17. Betty Boop
16. Gumby
15. Pikachu
14. Daffy Duck
13. The Powerpuff Girls
12. Fat Albert
11. Bart and Lisa Simpson
10. Cartman from South Park
9. SpongeBob SquarePants
8. Charlie Brown and Snoopy
7. Angelica Pickles
6. Fred Flintstone & Barney Rubble
5. The Grinch
4. Beavis and Butt-Head
3. Rocky and Bullwinkle
2. Homer Simpson
1. Bugs Bunny

Jerry Beck's picks for 50 Greatest Cartoons and Cartoon Network's picks for "50 Greatest Cartoons" and "Best We Got" marathons can be found here.