After a failed escape attempt the night before, it's the day of Linc's execution, T-Bag comes up to Michael and tries to make him feel worse. Sucre steps up to T-Bag and threatens to pound the rapist into the ground, and that "it wouldn't take much." T-Bag walks.
After being betrayed by one of his prison cohorts, Abruzzi breaks a lightbulb, sneaks up to the traitor, presses the shard of glass to his eye and delivers yesterday's news.
Micheal holding Warden Pope at knife-point in the climax of Season 1. The old man never saw the betrayal coming, which made Michael's sudden stone cold attitude towards him all the more epic.
Pope: You can't possibly get away with this—
Scofield: *brandishes knife* I don't think you want to find out how badly I want to get my brother out of here.
T-Bag's takeover of Sona at the end of Season 3.
Mahone killing the agent who murdered Mahone's 7 year old son. Mahone calmly tortures the man to make him apologize. Then as the man is about to launch into his mind bending 'we're not so different, you and I-' Mahone throws 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 3.
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)
When Sucre and Michael triumphally open the former's pack to check on Westmoreland's five million bucks, they find it to be filled with magazines instead. The scene cuts to T-Bag driving away in a used car as "Roll On Big Mama" plays on the radio. The flashbacks reveal that he switched the pags when no-one was looking, pretended to be upset that Sucre ran away with the money, hid before Michael could subdue him, and came back to collect the money once everyone had left. For once, Michael Scofield was Out-Gambitted!
Michael purposely rigging the escape tunnel to collapse and kill Sammy in Season 3. Furthermore, it is the first death that Michael intentionally caused in the series.
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.
Lincoln saving Michael and Roland in season four from a server room losing oxygen by calmly taking an axe from a nearby firetruck and breaking the server room window open with a single strike.
Almost everything Michael does in the first season at least, barring a few unexpected events, he planned an elaborate breakout plan that required him playing multiple people, including terrifying convicts and corrupt COs, like a fiddle, to ensure that he was in the exact places with the tools he needed, to break his brother out, the sheer amount of detail and complex parts required to make it all work is staggering.
Possibly one of the biggest cake takers is in Season 4, where Michael and co pull a big move on the Company in Selfless. Some classic lines, including:
Lincoln: Bet you wish you'd framed somebody else, huh?
