For rape scenes the ones in A Clockwork Orange, Pulp Fiction, Once Apon A Time In America and Deliverance were quite full-on.

As for violence, Nicky and his brother getting the shit beaten out of them was one of the worst, although the most disturbing part was seeing them getting buried while still half-alive. Utterly terrible.
In A Clockwork Orange when Alex is taken into the field by Georgie and Dim, dunked in the trough and beaten up his quite violent.
In Pulp Fiction, almost everything in the "Gold Watch" section is pretty violent.
In Gladiator and Braveheart the fight scenes are quite violent.
In The Shining the eleavtor pouring with blood, despite not being violent, is still f*cking scary, also when Halloran gets an axe in the chest.
In GoodFellas the opening, and speaking of openings, Savign Private Ryan's was pretty gruesome.
In Pulp Fiction in the car where Vincent accidently shoots Marvin in the face (the state of the car is the worse thing).

and

Reservoir Dogs, I'm surprised no-one mentioned the torture sequence (although there are probably worse ones around.)

-Penguin

Also is American History X worth taking a look at?