first of all, I'm not putting too much stock in this list, as IGNs reviews in general have been pretty :S to me
BUT- here are some interesting things I've noticed
1. A LOT of the top shows are action shows and 70s and 80s saturday morning cartoons. Personally, I don't think that these shows generally represent the best of the medium, and a lot of the saturday morning stuff seems to mostly be nostalgia.
2. Almost all of the top 10 except looney tunes were adult oriented comedies with extremely limited action. While they may be some of the best of the sitcom genre, I again don't think they fully represent the versatility of the medium, since a lot of them deal with similar topics and humor.
3. I'm pretty sure all the non-adult CN shows except for clone wars (which btw I have no idea why it was on there. It just seemed like more SW fan service to me) on there were either made by Genndy Tartakovsky or Craig McCracken. Granted, Genndy and Craig are some of the best cartoonists of the day, and my respect for samurai jack is boundless (it seriously deserves a higher place), its also the case that their shows were the only ones that really made a splash outside of the CN community. A lot of less known but still popular and good CN shows were left out , and even prominent ones like EEnE were neglected. It just shows how under appreciated CN is, even though their shows are some of the cartooniest shows around today, and the closest in spirit to the original shorts of the 50s and 60s IMO.
onowait Johnny Bravo was on their too. I'm not too big on that show though, but its OK.
4. My top shows to make the list that didn't make it
TMMoF
Billy and Mandy
Sheep in the Big City (one of the most under-appreciated shows ever, but also one of the best)