Several that spring immediately to mind have already been mentioned:
- The flagellation and crucifixion scenes in The Passion Of The Christ.
- The rape scene in Boys Don't Cry.
- The miming to Roy Orbinson in Blue Velvet.
- Whilst on the subject of David Lynch, not a film, but many of the BOB scenes from Twin Peaks.
- The kerb stomp from American History X.
- The circumsision (sp?) from Hard Candy.
- The ankle shattering from Misery.
The Green Mile, not for the execution of Del that everyone's mentioned, but for the evil smile on Billy's face after seeing the bodies of the two sisters. What's implied is definitely more disturbing than what's actually seen.
Likewise, The Human Centipede, but for the final scene with the front and the back of the 'centipede' dead, and the poor girl stuck in the middle of them.
Also, one of the later Hellraiser sequels, V or VI (can't remember which but it's subtitled Inferno) that featured hardly any gore and relied on implying the deaths, as well as being more psychological than hammer/slasher. IMO a great sequel to the franchise and the most disturbing.
One that I can't believe hasn't been mentioned yet that haunted me for a long time, is the scene from Jacob's Ladder where the demon surgeon injects Jacob in the centre of his forehead. Terrifying stuff.