* 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.