My vote is for willy wonka because it's not very clear whether the naughty kids live or not and also that scene near the end when Wonka is yelling at charlie and telling him he lost for stealing. Wilder's acting is so intense...it definitely scared me as a kid.
The scene that freaked me out as a kid was the infamous "boat ride".
If I'm not mistaken, I think that scene made Bravo's top 50 scariest (or was it top 100) scariest movie moments of all time.
And it's in a supposed kid's film!