Gargoyles was amazing. The movie (which shows the story of their "creation") and some of the early episodes can get surprisingly dark (but deep).
Another show along those lines is "Batman Beyond" (a dark "reboot" of Batman in which an aging Bruce Wayne enlists a young protege to be the next Batman in the near future).
In both shows (particularly Batman Beyond), if you ignore some obvious elements that point to them being shows for kids/teenagers, they almost seem like they were originally intended for adults, and then later rewritten to be targeted towards younger audiences.
If you enjoyed Gargoyles and you're still inclined to watch animated shows, please check out two of Greg Weisman's other creations: The Spectacular Spider-Man (not to be confused with the currently airing Ultimate Spider-Man [1]) and Young Justice (currently in its final season).
http://en.wikipedia.org/wiki/Gargoyles_(TV_series)