Something that I do commonly feel in some games in a weird sensation in my legs when I'm falling. Especially from very high distances in game where jumping high/falling is common and not fatal, like Prototype, or various super hero type games. It eventually goes away.. But I get a weird tingle/tensing up feeling in the core of my legs. It's very odd feeling. But in reality, I don't have any specific fear of heights or falling beyond what probably most people have on an instinctual level.
And something else I wouldn't really call it a phobia exactly, but a sort of anxiety, about games/movies where non-enemy women (civilians and such) are being hurt, killed, or whatever. Even in games where it's common to have a reckless disregard like Saints Row, or Grand Theft Auto. I try to avoid hitting women with my cars or stray gunfire. In general I try to avoid non-combatants as much as a I can, but if a man gets in the way and avoiding hitting him would be very detrimental to my goal I sometimes won't stop.
Back in response to others in the thread, I knew arachnophobia was pretty common, but not so much about fear of water or ocean. I never really thought about it but I guess that would make a lot of games pretty difficult. I know my girlfriend despises the spiders in Skyrim, and doesn't even want to see pictures with spiders in them. I think the problem is with the ones in games that are fast and climb on the ceilings, are jumpy and in general attempt ambushes. Because she has no problem fighting and killing them in World of WarCraft, even the giant ones. Those ones aren't scary to her.
The phobia that I really notice in myself is sometimes claustrophobia. Mostly commonly when I'm on a roller coaster and it uses those restraints that swing down and cover your chest and shoulders, especailly if they click down one too many times and gets tight up against me. I get pretty uncomfortable when it's a ride that has a delay at the end where you are just sitting there waiting for the train in front of you to move on. But being in tight places in games or small rooms doesn't bother me, just being restrained around the chest.