Irreversible. When the dudes being... um... "accosted" and his friend decides to help him out with a fire extinguisher. You guys can youtube that, because I'm saying no more. I literally shuddered just typing that.
Also, for some reason, the massive gunfight like a third of the way into The Rock disturbed me. I was kind of young when I watched it and it didn't hold much back.
EDIT: Ooh, brainflash. Silent Hill? Poor movie, yeah, but Pyramid Head literally RIPS a woman's ENTIRE SKIN off. It's messed up.
Another little lesser known one was from . . . 2001 Maniacs, I think it was called. Either way, a girl is about to go down on this guy sitting down in a chair. It's all normal, they're giggling and everythings calm, then the girl kind of looks down and starts fiddling, and then looks him in the face with this diabolical looking set of metal jaws in her mouth. Rest is self-explanatory.