For me it would have to be many short sences from saw 3 where the people that jigsaw capture and watches them escape from the contraptions in which they have to escape from.
The rape scene in Irreversible was horrible - I agree, and the (previous) subsequent killing in the gay club.
Also the animal slaughter in Apocalypse Now.
Another vote for American History X. Can't watch this film again - it's my favourite but it's so disturbing. I spend nights awake trying to get the sound of the skull be cracked out of my head.
Jorge Buttgereit's Nekromantik, several nasty scenes including sex with a corpse, animal skinning and suicide by stabbing whilst masterbating, pretty nasty all round.
Nekromantik 2 and Der Todesking are pretty nasty too.
The kerb scene in American History X is winning in this poll! closely followed by Irreversible.
American History X is IMO a great film. Irreversible I thought was a bit (no, actually a LOT) gratuitous.
Agree with Nekromantik that was gruesome.
American History X's kerb scene was horrific.
There is also a rape scene in "The Untold Story" where a handful of chopsticks is used which is not easy to watch.
I thought that the infamous "To know death..." scene from Flesh for Frankenstein was pretty shocking when I first saw it in the 70s, but I recently bought the DVD and the whole film is quite sweet!
The finale of Freaks is quite shocking.