A bunch'a things.
-Human skeletons, especially the skulls
This was the main thing that scared me as a kid, I couldn't look at one of them that I would immediately cringe and have nightmares thereafter.
I somehow stopped in 2007, don't ask me why.
-Primates;
After seeing that episode of Walking with Beasts with the Australopithecus I couldn't sleep for weeks. Since then Gorillas, Chimps and animals along the lines scared the crap out of me.
They don't anymore, though.
-Silence
As a kid I couldn't sleep without some familiar noise/music going on. Most of the times I still can't today.