Lily killing the Cheyenne that killed her husband, after already being shot in the hand and shoulder, and then pulling the arrow that shot her OUT of said hand and shoulder, to plunge it into the Cheyanne's neck. She then sews her own wound, and evades the other Cheyennes hunting her until she can get to safety.
Cullen saving Elam from being hanged, and their ambush of the tracking party.
Lily slapping her bitchy sister-in-law while making it clear that she killed the Cheyenne that killed her husband.
Durant Outgambitting Senator Crane, getting the man back under his thumb.
Reverend Cole DECAPITATES Sergeant Griggs with his own weapon after the latter threatens to kill Joseph Black Moon in the end of episode 9.
In the season finale, The Swede reveals he rounded up all evidence and history of Bohannon's crimes and delivered it to the government, which causes Bohannon to flee the railroad, and he did so in weeks, without any knowledge of Bohannon's past. Bohannon threatens to kill him, and he merely answers "Then I'll die knowing I was the one to take you to your grave." Bohannon backs off and leaves.
Bohannon pulling off a The Chessmaster to get his way Using the workers' wrath at Durant to get Durant to give him full authority, then using that authority to pull off a Xanatos Gambit bringing in 200 new workers to replace the ones on strike, leading to a fight: if the 200 new workers win, he gets his workers either way, if they lose, he just managed to unite all of his workers. The second option happens, which allows him to arm them against the Sioux. Meaning Bohannon managed to solve all the railroad's current problems with a single gambit: He now has his worker's respect, his workers are more united than ever and ready to take on the Sioux. And he did so in about three days. David Xanatos would be proud.
The thieves are robbing the railroad, which gives us a pretty tense situation and some damn fine action scenes in the middle of the ensuing battle:
Durant flat-out refuses to open the safe, even with a shotgun pointed at him. And when they mistreat Mrs. Bell, Durant pulls out a pistol and headshots one of the thieves. No wonder he is the leader of the railroad. He gets shot and almost dies immediatelly after, but he still deserves a mention for the sheer badassery of the moment.
Lily Bell shoots Hawkins in the thigh, giving Bohannon the edge in battle. Specially note-worthy because the woman barely knew how to shoot the gun and was shaking like Hell, yet she managed to get a good shot.
Thomas Durant loses his job and career by the end of season 2, in the season three premiere, he comes out of jail. Within less than one episode, Durant manages to get back on top of the business and becoming just as powerful as he was before with nothing but sheer guile.
Durant has comitted murder, and even he has no idea what to do, and is just left having a Villainous BSOD, feeling sorry for himself and overall a mess of a person. Cue Mickey walking through the door and teaching Durant how to do his business.
Mickey: I understand you're in need of a good magician. Someone who can make all your problems [[makes a coin disappear with a sleight of hand]] disappear. I know how you feel right now. You just killed a man and you don't know what to do. Your legs barely hold up, you can't eat, not even sleep. The whiskey...the whiskey seems to have no effect at all. (...) Now, you're not gonna run. You're not gonna call any attention to yourself. You gonna do exactly as I say, do your hear me?
Durant(Durant spent this whole time drunkely staring into the nothing in mysery and amusement'):....Do I hear you? (chuckles) You're...you're a saloonkeeper, a pimp, you run a bordello for God's sake! Why would I listen to you? He was...he was my friend.
Mickey: As far as I know, that's my job. It's gonna be some job indeed, but it'll all be alright. We're in America. You're probably not the first person to squeeze a bit o' lead into a US Senator. No matter. The magic...(Makes the coin from before reappear) The magic will save you this time.
Mickey then proceeds to do exactly what he promised: Saving Durant's ass without raising suspicion without breaking a sweat.
An episode later, after Mickey manages to fully solve the murder situation without leaving a hint of blame to himself, even outsmarting a Boston police officer, he shares this dialogue with Durant, a crowning moment of awesome for both of them:
Durant: What is it that you want, [McGinnes]?
Mickey: You do understand what this means.
Durant: It obviously means had I gone to jail, your odds at prospects in Cheyenne would have dimmed considerably. Do you understand?
Mickey(Cheshire Cat Grin): I am...but a simple irish man, seeking his fortune in the New World.
Mickey(Not threated in the least): You're threatening me? (Mickey glares, still grinning)
Durant: With a little bit of luck, you had the advantage on me. But I have been pushed aside, falsely accused, robbed, wounded and INSULTED ENOUGH! Now, if you rid yourself from these delusions, you may still have a future here. Otherwise, not. Good day, sir.
Bohannon is ambushed by some Mormons who seek vengeance. Not only do we see Durant, Bohannon and Fergurson fighting side by side, we see Bohannon cook up a strategy that would make Hannibal Smith proud to distract his foes. This culminates on Bohannon taking a stroll towards his many enemies in a clear field, gun in hand, calm, gunning them down with ease and calmly reloading his guns. Badass doesn't even begin to describe it.
Mickey deciding to give a proverbial fuck you to both Campbell and Durant and strike his own path to fortune independant of them (and quite possibly against them), which is almost a mundane version of Did You Just Flip Off Cthulhu?.