I don't really know that many scary cartoons any more because of all the ones I knew are gone from this thread, I do think that Mark Twain's cartoon with death and the clay village is scary especially since it's not meant to terrify.
When you think about it though, Walt must have been quite a dark guy, most of his early works are terrifying but hidden well with cute characters, look at this article.
http://www.film.com/features/story/w...-side/24013017