2 scenes in particular:

When I was 3 or so the Pinocchio scene when Monstro came out scared the shit out of me until I figured out it wasn't real lol.

There was also the scene in Alien Ressurection where the guy's head gets popped (they removed that on in the TV version and I can see why.) by the alien. Though this one made me wanna lose my lunch more than freak the hell out.