* 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).