My favorite is nearly any major cartoon set in the same universe as Batman: TAS, though I haven't seen as many of those cartoons as I would like.
I don't think any of the X-Men cartoons were all that good from what I've seen, but in X-Men: TAS' case, it may just be because the most recent episodes I saw were the first eight, when they were just getting started.
Spectacular Spider-Man and Spider-Man Unlimited are the only two Spider-Man cartoons that actually use their inherent potential to be good, while the others just sucked, even though SSM's art style is kind of lame.
Oh yeah, and Transformers Animated is good, if that counts (The autobots were referred to as "superheroes" in season 1). Though their art style wasn't very good either.
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Why the hell don't action cartoons use realistic art styles anymore?!