The Last Days of Foxhound contains a very large number of these, but the standout one surely has to be where Liquid beats the living crap out of Grey Fox with a whacking great hole in his chest induced by a sudden attack of sword.
Liquid: The fuck are you lookin' at, chief? Raven: Nothing!
Starting here, and ending here, Ocelot handing Mantis the most devastating defeat of his life using nothing but his silver tongue, while simultaneously revealing that every time Mantis thought he had the upper hand, Ocelot was actually playing him like a true Magnificent Bastard. Also notable for what is possibly the best comeback ever:
Mantis: I mean, you must spend every day pretending to act like you're falsely letting on that you aren't not unbetraying someone you don't not purport to allegedly not work for but really do! How do you keep this shit straight without having an aneurysm? Ocelot: (shrug) Practice.
Mantis: I'm torching everything that moves and almost everything that doesn't. Liquid: Why? Mantis: Why not? Liquid: (Stunned Silence. Beat.) Alright, but why are you doing it now? Mantis: Much better question.
Raven disposing of the team's latest target by shooting him in the face. With a tank.
Raven may also deserve one for staring down Big Boss when he was possessing Liquid's body, knowing that the guy could probably tear him to pieces in hand to hand combat if things got started up. And Raven still stood his ground until the tranq finally kicked in. Cue the Post-Victory Collapse.
Liquid Snake coming up with a plan to stop a hostage situation nonlethally in the drugstore. He defuses the entire situation without a shot going off, in stark contrast to his usual approach of hitting things until they die. Granted, he should have paid more attention to the dosage of the pills... But everyone made it out fine.