Assassinating Corporate Kelly in the "non-lethal" path. Since you have no sword to directly kill him, what do you do? You drop the ceiling supporting spotlights on his head. While the final animation has you using your sword, even if you don't actually have one, doing this is incredibly satisfying.
The Fall of Hessian Tower has you triggering several gas taps throughout a building to fill the whole thing with gas. You then drop a broken transformer on top of the whole thing. The build-up and the payoff are nothing short of satisfying.
Assassinating Count Karajan. You've been tearing through Karajan's finest troops and top level security systems, after making sure he won't have any chance to escape again, by the time you enter the count's manor he really starts losing it. After all crap he put you through it's very cathartic to finish him off.
The Marked Ninja standing against Azai after dealing with the Hessian Services. He refuses to commit suicide and escapes from a room full of people trying to stop him with a simple smoke bomb.
Perhaps not for the Marked Ninja, but one for Azai. After realizing his star pupil has fallen to madness, not only does he keep his calm after the marked ninja returns and finds his way to the inner garden, but he doesn't even bother to fight the marked ninja, inviting him inside, giving him a sword, and then kneeling there to let the marked ninja make his own decision, and doesn't even show a single sign of fear during the whole encounter.