I hate big spiders and being up off the ground where I know I'm not protected. Like others have said, I can stand atop the Empire State building and look down, but going up the ladder to hang Christmas lights makes me very uneasy.
The one thing that I truly dislike are looking at sunken/run aground ships. Like watching things on the Titanic where they show it sitting at the bottom of the Atlantic or seeing that Italian cruise liner on its side a few months ago makes my skin crawl. I love boats and being on the water, but seeing stuff like that just creeps me out.