Starting at No 5 and working my way down most disturbing scenes would be these.

No 5 Anything to do with the latest star wars incarnations. Lucas is so obviously dark side what with the hype and marketing machine not so much a disturbing scene as a whole ethos of grab the loot.

No 4 When they find the baby in trainspotting

No 3 The lack of emotion in shindlers list by the man in charge of the camp (the rifle scene)

No 2 Any scene in event horizon

No 1 Deliverence need I say more