well, its not western animation, but the demon in the mirror from the Unnatural History episode Now You See Me scared the piss outta me.
In addition: Ultimate Kevin, specifically that Kevin went from recovered villain to a sociopath who can phase through things and is Implacable besides. His methods of attack also brought a certain other power gathering juggernaut to mind...
For me, everything that's my Fetish Fuel, when seen on TV, is Nightmare Fuel. Not exactly sure why, but there you go.
I think TUFF Puppy is pretty creepy. Did you see the flashback where Agent Kitty ate a magician? Either she got her stomach pumped, or she flippin' killed someone in a rather gruesome way. A couple episodes later, a villain almost succeeds in killing Dudley the same way.
High Octane Nightmare Fuel, on the other hand, rarely gets me. Things like Flapjack just don't creep me out as much because I know they're trying to creep me out. For me, most intentional horror comes out as narm or squick.
I must be cruel, but to be kind That bad may begin, and worse be left behindIn the My Life As A Teenage Robot episode See No Evil, a giant eye villain accidently pokes himself with a pointy stick. The very thought of something so painful made me shiver as a wee one.
signature lineThe two transformation sequences in Wallace And Gromit: The Curse of the Were-Rabbit terrified me until I was 14. Now I look at them and go "This scared the crap out of me in the theatre?" but they kept me away from that movie (the rest of which I had loved) for five years.
Looking for some stories?The very last second of The Simpsons "Treehouse of Horror X" when Homer and Bart eject themselves into outer space and their eyes bulge out
Took me forever to ever wanna watch The Simpsons again after that

I dont think there was anything that scared me as a kid, but I do remember a few things on my younger brother was used to be scared of. He was nearly terrified when Nicodemus was explaining about NIMH.