Here's a few series I've found have aged spectacularly well (watching them today is no less enjoyable than when I was younger):
Gargoyles
Dark & mature themes, interesting characters who are suprisingly complex, a long-running and well-written narrative, excellent & surprisingly use of literature & mythology ... all from a Disney kid's show? Yeah, that last detail doesn't make much sense; nevertheless, it was an excellent series.
The Tick
The superhero spoof show; featuring the titantic, blue, nigh-invulnerable, and dim-witted Tick taking centre-stage. Quite a few of the gags in the show were very adult-oriented (i.e.: American Maid accusing Dieflater Mouse... uh, the bat guy of having a "fear of commitment"), which flew over the kids' heads. Good use of more intellient humour as well.
Earthworm Jim
Another superhero spoof show, albeit more zany than the Tick. Based off the video game, it still did a great job of lampooning everything it could. Having one of the catchiest theme songs ever certainly didn't hurt it either. Very silly, but all in good fun.
There's quite a few others I could mention as well, but not enough time at the moment.