There's not really any adult cartoons that I would rate highly right now. South park and the Simpsons have both been great in the past, but are now just shadows of their former selves. It is hard to run for as long as they have and stay fresh. I used to like Seth MacFarlane's shows too, but I think my sense of humour has changed over the years and I don't find them funny any more. The new episodes of Futurama are pretty funny, but they're hardly groundbeaking.
Historically though the Simpsons is an obvious choice, I think series five to nine may be some of the best comedy writing ever. South Park too, there are just too many great episodes. I Am Not An Animal was a really funny one, check it out buy the DVD, it's a great cartoon for adults.
On another note, does Monty Python's flying circus count?
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I forgot, the YouTube user Doki66 is definately worth checking out. His cartoons can be strange, but they can also be pretty funny (they just take some getting used to).