Sorry, I know you don't want to hear this complaints, but I need to say it: Transformers at number 3 above Looney Tunes kind of kills any right you have to claim your list is better than IGN's. Major fail there.
Two more comments:
Was IGN's list really biased towards anime? I count only 13 anime shows on the list, only 2 in the top 25, and only two series seem particularly out of place (Naruto's way too high if it deserves to be on the list at all and Afro Samurai certainly shouldn't be there, especially since Samurai Champloo isn't and did the same thing a dozen times better with actual character development). I do know my list would probably have more.
And Tiny Toons and Animaniacs coming out during a "dark time in animation"? To me, it seems like the late '80s/early '90s were actually something of a rebirth of animation. I mean, think of all the good stuff coming out around that time: in addition to those two shows, you have Batman: The Animated Series setting the bar for action animation, The Simpsons singlehandedly reviving the primetime cartoon, the Nicktoons going in all sorts of different directions (and the best of them, Rocko's Modern Life, somehow didn't even make the list!), Disney was doing both the Disney Afternoon and their great run of musical feature films, serious anime started coming over stateside after Akira. What was happening before that? A lot of toy commercial shows that honestly aren't very good. A few gems here and there as there always are but it wasn't a very good time for animation in general. If things seemed like they become worse, it would seem it's not because they actually were worse, they were probably better than any time since the golden age of Disney and Warner Brothers, but rather that that was the time you developed taste. Seeing as I'm 18 and either as old or younger than all the cartoons I was just talking about and wouldn't discover them until much later, I think I can judge these matters fairly.
For the record, my top twenty would probably look something like this:
20. The Flintstones (certainly deserves a spot for its positive influence but never really liked the show much myself; also, how is this what legitimized animation when it was followed by about twenty years without any sort of successful successor in terms of adult animation? it seemed the theatrical era animation was more consistently adult-friendly than the stuff that came after The Flintstones)
19. Rocky and Bullwinkle
18. The Powerpuff Girls
17. Popeye
16. Fullmetal Alchemist
15. Rocko's Modern Life
14. Samurai Jack
13. FLCL (if Looney Tunes counts despite being theatrical shorts aired on TV, then this video series aired on TV counts as well)
12. Animaniacs
11. Neon Genesis Evangelion
10. Pinky and the Brain (gets ahead of Animaniacs due to lack of crap segments like the Hip Hippos and Chicken Boo (who apparently was thought up by the same madman who invented the Geico gecko...))
9. Justice League/Unlimited
8. Invader ZIM (how did this miss the list?)
7. Avatar: The Last Airbender
6. Paranoia Agent (not an influential show by any means, but a brilliant one that deserves to be listed for quality alone)
5. Batman: The Animated Series (I actually haven't watched that much of this one, and I'm more of a Justice League fan myself, but I can see why this needs to be in the top 10)
4. Futurama
3. The Simpsons
2. Looney Tunes
1. Cowboy Bebop (for its consistency, mainly; of course The Simpsons and Looney Tunes were bigger and at times better, but they had a lot of moments they weren't so great, and Bebop is about as close to the perfect cartoon as you can get in my opinion)