Shepard gets a brilliant moment with his "The Reason You Suck" Speech to Miranda and Jacob in chapter three of Razor's Edge, where he flat out states that the Normandy SR-2 is his ship, his mission, and that if either of them tries to undermine his authority, he'll "Throw them in the airlock and see if The Illusive Man has enough bugs and failsafes to save them before he hits 'cycle'". Bonus points for delivering this speech in a calm, cool and collected manner.
Shepard calms Grunt down from his blood rage by standing his ground when Grunt charges him, flipping Grunt over him and slamming Grunt into the floor. Shepard then jams a pistol into Grunt's neck and stares him down until Grunt cools off.
After Tali has a grenade explode in front of her face, Shepard goes into Tranquil Fury mode and completely kicks the Shadow Broker's ass without weapons. Better Than Canon indeed.
What she'd been watching wasn't a fight. It was an execution. It had been a forgone conclusion from the second it began, the only question was how long it would take for Shepard to finish it once and for all.
And while Shepard is beating up the Shadow Broker, Liara calls Garrus:
Daro'Xen: "Should you not be defending your Admiral, marine?"
Kal'Reegar: "I only see four Admirals in this room. And one stupid gen'ro'sa that pissed off the only non-quarian that's given a damn about us in the last three hundred years," the marine responded coolly. "Ma'am."
After meeting the Rachni Queen on Utukku, Shepard must make the choice of whether to spare her or kill her. However, the Queen has prepared for both eventualities, and offers Shepard her own choice: let her live and she will stand with the combined galactic forces and unleash the full might of the rachni against the Reapers... or kill her, and set in motion a massive Thanatos Gambit that will guarantee the Reapers' destruction in the next cycle.
Saren: "It wasn't just for me. I thought I could save the galaxy."
Shepard: "You can't save something that you don't have a stake in. All you ever saw was your own hate. But it's over now. Do it... but I hope whatever is left of you goes back to the Reapers and tell them that I never stopped fighting. Show them that one person, one human can defy them."
Just as Kai Leng is about to finish off Thane, in full view of the Council and most of the Normandy crew, Shepard makes his triumphant return from the dead by disarming Leng, shattering his wrist, then using his fist and stabbing Kai Leng with an unheard of biotic power!
Kai Leng: You're dead, Shepard! I saw the reports! From your own crew...you were dead!
Shepard: Death and I have established an equitable working relationship. (creates arm-length BIOTIC BLADE) Why don't I introduce you.
After the Cerberus siege of the Citadel has been repelled, Garrus goes frantically searching for Kasumi, who was badly injured by a bomb. Once he tracks her down to the hospital she was taken to, he identifies the turian doctor who was operating on her and asks how she's doing. Said doctor assumes her injuries are the result of rough sex and has a less than approving opinion of Interspecies Romance. Garrus puts him in his place:
Any offensive diatribe the doctor had been going to continue with was cut off when Garrus whirled on him with amazing speed, wrapped a hand around the older turian's cowl, and slammed him into the nearest wall with a deep throated snarl.
Garrus: "I do not give a damn about your opinions on anything, you backwater colonial fuck, other than on the current medical status of the woman you operated on! Do I make myself clear? If not, I have plenty more petty abuses of power I can get into starting with removing your face-plates with my talons!"
Shepard's speech to the Citadel after his return from the dead, especially the last bit:
"My name is Johnathan Shepard. Twice the galaxy has declared me dead, but I still endure. I fight for the future of not just the Council or the Alliance, but for all sapient life in this galaxy. The Reapers think of themselves as gods. They would have us submit to slaughter because they demand it. But I stand before you now to deliver a single message."
After being ignored by the other admirals, then nearly killed on Rannoch and forced to abandon his men, then faced with Han'Gerrel's stubborn refusal to back down in the face of death, Zaal'Koris has had enough.
Zaal'Koris: "If (Shepard won't destroy you,) then I will, Gerrel! You have called me a coward, a suit-wetter, a sympathizer! But I am Admiral and I have not forgotten that our first duty is to our people! With that power and responsibility I am ordering you to stand down or by the Ancestors I will be the one that orders your ship turned to scrap! This war is over!"
Zaeed pulls off a big time Dying Moment of Awesome when he volunteers to be a sacrifice to clear out the hundreds-strong horde of Adjutants blocking the way to Afterlife by detonating an explosive that ruptures a plasma conduit and floods the whole area with superheated plasma. After, of course, making sure to down almost a dozen of them with pinpoint shot from a pair of pistols.