Heights, as a kid I used to go on top of grain bins, and corn silos; now even going on the roof of a two story house gives me the frights.
Also raccoons, had one get in the attic a while ago, and I just kept picturing him falling through the ceiling of my bedroom and landing in bed with me. That one may not have been irrational, waking up with a pissed off raccoon would have been bad.