I've always had this problem. I play a game like FEAR or Condemned and its scares me from time to time, but for the most part I'm fine. However, the way the enemies are designed in Minecraft creep me out. The blocky crude 3D look is very very unsettling to me. I have yet to confront one. I just hide in my house and refuse to find them. I'm not looking forward to digging into a dark cave system. I've had this "phobia" I guess ever since I was younger. When I played Outlaws of the PC, the 2D spiders fucking scared me. If I ever ran into a group of them, I'd hit ESC and quit/restart.   
 
I'm 19 now. This is retarded I know. But the first time I was outside and turned around to see a creeper coming at me with his face.....I was so freaked out. I was happy when he exploded. Means I didnt have to look at him anymore. 
 
Anyone else have this issue at all?

This video will be the opposite of helpful to you, but it is relevant and just too funny not to post. Sorry if it had been posted before, I've not been keeping up with the Minecraft threads.
  

" This video will be the opposite of helpful to you, but it is relevant and just too funny not to post. Sorry if it had been posted before, I've not been keeping up with the Minecraft threads.
  

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They're intimidating at first but you'll get used to them, obviously once you've faced your fears head on. Nothing's as worse as your imagination. 
 
also, MAN UP. 

" This video will be the opposite of helpful to you, but it is relevant and just too funny not to post. Sorry if it had been posted before, I've not been keeping up with the Minecraft threads.
  

"

Face one and get over it. Worked for me.
 
I still jumped out of my chair tho when I came across a skeleton in one of my cave systems...freaking skeletons.

You get used to them, but the ones in caves still freak me out, they come out of nowhere.

" This video will be the opposite of helpful to you, but it is relevant and just too funny not to post. Sorry if it had been posted before, I've not been keeping up with the Minecraft threads.
  

"

I get creeped out by the noises they make in the caves. I don't really like the darkness, so I spam torches, then run and hide and wait for the monsters to come to me. I never go to them, haha.