1. Elephants on Parade - When the mouse and Dumbo get drunk and then the weird shit happens. As a kid, that shit fucks you up.
2. The part in Pinocchio where they're in Pleasure Island and all the boys are being turned into donkeys.
That was scary...and a bit fucked up for a children's cartoon.
3. In an episode of G.I. Joe (the cartoon) called “There’s No Place Like Springfield", Shipwreck is in a simulated future (of course fabricated by Cobra) where everybody around him melts and his family tries to kill him. The oddest episode I've ever seen and arguably the most fucked up. IT really had more of an impact than I thought at the time.
Here's a small clip of the episode. I wish I could find the whole thing. Add it to my "To Be Torrented" list.
It wasn't until my AutoCAD class in college, where I happened to overehear some guys behind me talk about the episode, that finally reminded me of this episode and put all the pieces of it together (name of the character, what's the plot of the episode, etc)
By the way, this episode makes the list of at this blog, The 10 Most Insane, Child-Warping Moments of ’80s Cartoons