Snakes and ghosts.

I fear parts of games that are boring.

Spiders!

The Ghosts from the F.E.A.R. games were pretty damn scary so I agree with that

This.

The worst part is that I always end up dying from some stupid mistake due to the panic even when time is ample.

Nothing scares me. I take everything as a challenge. That I can beat.

running out of ammo. That always sucks! Especially in a game like Modern warfare or Fallout, etc.

You ran out of ammo in Fallout 3?

Open-world games when you wander into a battle with something waaaay more powerful than you (might be why I don't care for FF7), I also don't like the feeling of "Here's the world, you get no direction, just have fun" makes my stomach ache. Timed events. The regenerator from RE4 (especially the spikey one). Crappy puzzles that don't have any hints in the game to solve them (Castlevania 2 comes to mind, kneel next to this lake and type in a code, that you're just supposed to guess?!). Too much trial and error in puzzles, particularly if error results in death and long load times (Tomb Raider anniversary, I'm lookin' at you)

2 words...

Re-spawning Enemies