Ren and Stimpy and Rocko's Modern Life both had stuff that was bizarre and only allowed in a kid's show because it was over their heads.
Batman TAS and Gargoyles both had some heavy shit. The latter also had a guy die by having fire erupt from behind his eyeballs, and a scene where a surgeon explains a gunshot wound in visceral detail. God I love that show.
If you like weird old SF books, the guy who wrote TAS and Gargoyles (RIP J. Michael Reaves) did a space-noir called Darkworld Detective, it's pretty good. Obviously unrelated to Batman though.