I was always scared of lifts. Fit with my fear of heights, I suppose. I always had to use the stairs instead. Made those inner-city stations with only lifts a pain in the arse
Also, I used to be scared of giant brains (wait, don't go!). I had this horrible dream when I was really young, I remember being chased down a hallway by this giant brain... it disintegrated me and then the chase repeated itself. Each time I'd almost get to the living room to warn my parents, but the thing would disintegrate me JUST as I got to the door, every time. I think it was because of a boss on one of the old Shinobi games on the Mega Drive... on which note, I remember the last boss on one of them had an evil laugh that scared the hell out of me.
Games scared the hell out of me as a kid, actually... anything Silent Hill scared me. I'd imagine Pyramid Head coming to kill me or whatever when I was trying to sleep. I was a nerdy, scared-y kid :O