All the torture scenes in Panama, but particularly Sucre's. He is forced to dig his own grave and then interrogated while being buried alive. Doubles as a Moment of Awesome, since Sucre refuses to confess where Lincoln and Michael are.
All the torture scenes in general, especially the cold-blooded one by Mahone on Wyatt, regardless of how deserved it was.
Any scene where they take out the saw and the plastic bags in the context of disposing a corpse (who is still alive, by the way, and listening).
Having to listen to your little brother slowly lose his mind in solitary, when you are only in the next room over but can't do anything to help. That would seriously screw with your brain.
Sara holing herself up in terror in the infirmary during the riot in Season 1: she's cornered and unable to escape through the window (it is a prison, after all), none of the authorities outside can hear or see her, the guard who's supposed to be protecting her is threatened into not reporting that she's in danger, she has no real means to defend herself outside of some broken glass, and the infirmary is surrounded on all sides by violent convicts excited to rape and likely murder her as they slowly start to break the glass and work their way in, having started fire, on top of everything.
Lincoln listening via phone to Veronica being shot. Don Self, as big of an asshole as he is, is forced to go through the same, hearing his wife getting killed, while he's totally unable to do anything about it.
LJ learning that his mother and her partner are both killed, and later discovering he's framed for the double-murder.
T-Bag forced to bite off the stitches of his artificial hand in order not to get caught by the police called by Bellick and Geary.
