Personally, I would have replaced El Tigre with Danny Phantom, and switched SpongeBob and Avatar’s spots. I enjoyed Avatar A LOT, but I think SpongeBob is a little more deserving of the #1 spot – seeing how it’s still #1 on all of TV for kids (and a hefty amount of adults, too) in its 10th year.
I think people get caught up thinking about OddParents post-Channel Chasers episodes they forget how everyone seemed to love the show before the movie. Why should the show get booted off the list because not everyone loves the more recent episodes? For several years, OddParents was a very close #2 to SpongeBob in ratings, and it really stayed that way until the “cancelation” in 2006. Plus, 2007’s OddBaby special was HUGE, getting more total views in one sitting than any SpongeBob special ever has.
I think Jimmy Neutron deserves that #4 spot. It is one of the only comedy-driven shows that really got better as the episodes went on. Plus, it must have been popular enough for Nickelodeon to go through with a spin-off (Planet Sheen).
While Penguins of Madagascar is VERY good, I think it’s best to leave that for a “Toons of the 2010s” list. Just like NO ONE would have put SpongeBob on a “Best of the 1990s” list, since there were so many other shows that lasted longer in the decade. I’m sure Penguins will extend into the 2010s far enough to reign in that decade like SpongeBob has in this (unless SpongeBob just continues to dominate in the next decade too!).