* All the torture scenes in Panama, but particularly [[TheWoobie Sucre's]]. He is forced to dig his own grave and then interrogated while being buried alive. Doubles as a CrowningMomentOfAwesome, since Sucre refuses to confess where Lincoln and Michael are.
* 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.