There's no question that The Simpsons is #1. Seasons 2-9 (yes, 9 is still classic) are so good that no amount of bad seasons could possibly taint its rightful place as the greatest animated series.
I'd put Looney Tunes at #2 rather than Batman, but that's nitpicking. Also, I haven't read the whole list, but if it's true that Rocko's Modern Life is not on there, that is a travesty; that show was the true triumph of early Nickelodeon (it was certainly a million times better than Ren and Stimpy). Hey Arnold! could also stand to be on the list, but it's not an unforgivable omission.
If Family Guy had never been resurrected, it might have deserved a spot fairly low on the list (80's or 90's, maybe); as it stands, I honestly don't believe that it deserves a spot, and it's not due only to my dislike of the show.