The most disturbing movie rape scene that I have seen is Gaspar Noé's Irréversible starring Monica Bellucci.
Yeah, that one wrecked me too.
Irréversible
The Accused
Casualties of War
Bastard out of Carolina
The Informant
All of these (off the top of my head) include rape scenes that still haunt me. Seriously, I'm a total wuss with that stuff. I can't handle it. And now I basically avoid watching anything that I know has scenes like that in it (like "Boys Don't Cry" or the uncut Zombie "Halloween").