@ Seth: I do that too. I've been doing it recently though, having vivid recollections of missing half of an entire semester of classes (or at least one course). I think I'm going crazy, let's just hope not as bad as you!
Chojin already posted my most scarring childhood scene. I've seen Little Nemo and Dark Crystal and pretty much everything mentioned in the thread (except for that Maurice Sendrak thing where they cook the kid, fuck that's spooky) but nothing stands up to George Pal's Puppetoons.
He had a string of stop-motion hits, and my family got them for me on VHS when I was really, really young. There was one cartoon involving a maestro who is almost cannibalized that I would reluctantly watch, but would cry silently the entire time. My nightmares had color for the first and only time in my life, my own marionette hell. The only cartoon I liked on the tape was about a tuba. His name was tubby. Nothing shitty happened in that one, but Tubby sure was a spooky fellow:
Look up George Pal's animation stuff. I can't find any of it on Youtube (other than the still frightening John Henry clip), but most of it is extremely unnerving. He had a racist stint too, animating a young boy named Jasper:
The final one was called Hoola Boola and involved a tropical island and a dickhead named Jim Dandy.
Here's a video of it. Note the animation of the mouth as they speak, that really got to me.
EDIT - Going a bit off the path, Chojin and I also played through Braindead 13 together. I'd wanted it as a kid, but I think it's safe to say that I would've been scarred for life had I seen some of these deaths:
ANOTHER EDIT - Sorry to monopolize the thread, but I found the rest of the Puppetoons. Guess someone uploaded them while I wasn't looking.
Here's Tubby the Goddamn Tuba, the least scarring of all his abominations.
And The Little Broadcast, the one with the cannibals.
There are some scenes missing from both, but those are the meat and potatoes of the things.