There seem to be two kinds of cartoons when one talks about "the best": there are the ones that you appreciate as genius and there are the ones you grew up with. Sometimes they overlap, sometimes they don't.
The cartoons I grew up with include: The Magic School Bus, Pokemon (season 1), near the end of Hey Arnold!, The Grim Adventures of Billy and Mandy, somewhat Rugrats (at the time, I despised the show, but now I look back and I really like it), Powerpuff Girls, Dexter's Laboratory, the last showings of Cow & Chicken; Johnny Bravo; and CatDog, again the end seasons of Doug, Spongebob Squarepants (of course), and that's all I can think of.
The cartoons I currently admire and enjoy watching:
Animaniacs, Pinky and the Brain, Freakazoid! , Spongebob Squarepants (the pre-movie seasons are the best/better/good, period), Road Rovers, Dilbert, The Simpsons, Futurama, South Park, Dexter's Laboratory, King of the Hill, Johnny Bravo, The Grim Adventures of Billy and Mandy, Rugrats, etc.