And T-Bag's takeover of Sona at the end of Season 3, truly cementing him as a Magnificent Bastard.
Mahone killing the agent who murdered Mahone's 7 year old son. Mahone calmly tortures the man to make him apologise. Then as the man is about to launch into his mind bending 'we're not so different, you and I-' Mahone kicks him off a jetty, to his death, without a word, and calmly leaves
Michael in season three hiding a Batman Gambit inside his escape attempt to make sure all the people he doesn't want with him don't make it out.
Sucre refusing to tell the Panamanian police where the brothers are while being brutally tortured at the end of Season 2.
The frequent reunions of Michael and Sucre - most notably after the 'double-cross' in Utah.
Michael: Adios, amigos?
Sucre: (long pause, then grins) Too much?
Michael: You were great. (bro hug)
Michael purposely rigging the escape tunnel to collapse and kill Sammy in the third season.
Sammy himself had an awesome moment in the beginning of the third season, by beating and snapping the neck of another inmate, shocking the usually stoic Michael.