Mine's a little specific, deep water, but it needs to have certain qualities.
Like swimming around Vashj'ir in WoW is fine, the water world in Folklore had no effect, in real life I enjoy being underwater and my only fears are ocean level and the fact I'm a weak swimmer (which is less a fear and more an intelligence to stay away from deep water in that case).
But some places, Fatigue water in WoW, Deep places in Minecraft, looking over the edges of world, staring into voids, under water in Oblivion...
That monochrome, featureless, dark, and endless space just robs me of my senses.
I can't feel it, my hearing is all muddled, and my sight has been taken, my movement slowed, my life draining, my sense of gravity non existent for my Avatar's orientation.
It feels like death and alone.
Like being left, forgotten, imprisoned, and defeated.
I do not deal with this fear.
I take a deep breath and clear my mind, I focus my will and dive in, then I panic and choke and want to cry and do everything in my power to accomplish my objective within seconds or I leave.
It's not always that bad, sometimes I don't feel as effected by it, but others? No, just... No.
One great story where this improved a game for me though is Oblivion in "Through a Nightmare you are trapped in Henantier's dreams where you need to overcome challenges related to his psyche to assemble his mind so you may both escape his head.
Perception? Easy.
Patience? No problem.
Resolve? Of course.
...Courage? I initially thought I had it until I stepped up newly restored weapons in hand and opened that urn with quest related item for this challenge.
"Water Breathing Potion"
My heart stopped, courage faltered, and I had infinitely more respect for the challenges I was facing.
I did take a deep breath and dive through the black channel to mine, and my new friends saftey.
But I'll be damned if it was easy.