I give props to penguinwizard for mentioning Earthworm Jim, and in the very first reply to boot. I haven't seen it since it was originally airing, but I will still confidently say that it was one of the best shows I've ever watched. Earthworm Jim and the Madballs: Gross Jokes probably shaped my sense of humor as a kid more than anything else.
Warner Bros. had an extremely strong period with Animaniacs, Pinky and the Brain, and Freakazoid. And Tiny Toons, which now that I think about it probably spawned the streak of awesome.
Samurai Jack is extremely impressive, especially how it's not afraid of silence. Cartoons that don't need to rely on nonstop dialogue are precious things. And extremely lengthy, good fight scenes.
My favorite anime are The Melancholy of Haruhi Suzumiya, Yakitate!! Japan, Bobobo-bo Bo-bobo, Kogepan, Excel Saga, Midori no Hibi, Sayonara Zetsubou Sensei, Sex Demon Queen, Full Metal Panic? Fumoffu, G-On Riders, maybe. Welcome to the NHK is pretty good.