Some kind of cave dwelling shark boss in a Tomb Raider game gave me the water phobia, I can't deal with it at all... even when I was playing Jaws Unleashed (wherein YOU play the biggest shark out there) I was freaking out like crazy.
It's carried over pretty bad, I went into all out panic at the START of a tomb raider game cause it dumped you in the ocean and I couldn't see anything. I'm paranoid of water in all other games, I can barely function in water on WoW even when you've got everyone's health bar visible within a five mile radius and track beasts on.
I don't fear it in real life, just shadows, that's carried over to games, and it's worst in Skyrim at the minute cause EVERYTHING has a flickering shadow that looks deceptively like someone is stood immediately behind your sneaking ass.