Well, since I'd consider heights and spiders and stuff to be "rational" fears, seeing as how falling from a height can kill you and there are some poisonous spiders:
Tall things. I have no idea why, but looking at tall things gives me vertigo and turns my legs to jelly. We tried to walk across the golden gate bridge at night once, and I couldn't do it because those towers are fucking massive. I'm sure my fear of heights, and water didn't help, but yeah.