The fire extinguisher and tunnel scenes in "Irreversible".
The eyeball slicing is also very disturbing. I think I've seen it just once, after that time, I always look somewhere else when the scene is going. Buñuel -a spanish expatriate in France after spanish civil war- was an specialist in shaking and provoking.
Talking about "saving private Ryan", there is an scene that bring a tear to my eye everytime I see it. The mother falling to her knees when she sees the car coming her way, anticipating what the news were.