Movies do have some really awful stuff in them, don't they?
I agree that anything with a rape scene is very hard to watch and it really neeRAB to be justified in the context of the movie to allow such a scene to be shown (e.g The Accused, Boys Don't Cry, Monster.)
Scenes of torture and mutilation are always hard to stomach - the Texas Chainsaw Massacre, Wolf Creek, Funny Games etc.
Gory scenes in horror movies have been done to death (excuse the pun) but I was very disturbed when I first saw John Carpenter's remake of The Thing.
But some things are disturbing because they're just unremittingly evil. Earlier in the thread someone mentioned Come and See. The scene where the boy witnesses a group of Nazis setting fire to a church full of people is really horrific.