Hmmmm, let's see...
The scenes featuring the villian in
We're Back! A Dinosaur's Story freaked me out quite a bit, but it was his actual death in the movie that really messed me up for the first day I saw it.
Some of the more darker scenes in
The Little Mermaid really creeped me out in parts, I'd say which one especially creeped me out a lot but I fear it might spoil a bit of the movie and also, I can't remember how to make the spoiler tag work again (I know, it's been a while :sweat

so I'll just leave it at that.
From
The Pagemaster, the Dr. Jekyll and Mr. Hyde scene and that very short Moby Dick scene both really frightened me for the first 3 or 4 times I saw the movie.
The TV movie
The BFG's opening scene scared me quite a lot as well, but I soon put that aside when the "Whiz Bang! Whiz Pop!" song started to play.
And finally, I can also remember that single moment in
Toy Story when Sid's dog wakes up when he hears (I presume it's a he) Woody's string pulled really making me jump!
Heh, apart from those, I wasn't scared of any animated movie I saw as a kid.