Conrad Marburg from Alpha Protocol. Not as a boss (though he is hard enough), but rather what he does in the story. Granted, he is supposed to make you feel that way.
After playing cat-and-mouse with him for a few missions, with him being an arrogant git the whole time, you finally get to the endgame for that region, the museum in Rome. Towards the end, you are informed that he has captured Madison, someone who is under your protection, as well as a potential love interest. She is in one wing. The bombs he has planted to help incite a war are in another wing. You have to choose. If you choose to save Madison, she gets pissed at you and leaves, so I always choose the bombs. After you defuse them, Marburg shows up with Madison. You yell to let her go. Marburg agrees...then promptly shoots her in the back for no reason. And then, he has the sheer balls to say her death is all your fault, a sentiment that Leland echos in the next cutscene. And then he calls you arrogant, to which you can respond with one of my favorite lines.
"Arrogant? No, arrogant is shooting an unarmed woman in the back and assuming that means you can take me out."
Unfortunately, if you have not done your utmost for the entire game to piss Marburg off (which means you cannot be a stealth character or a Professional, since he respects an agent who keeps a low profile and a professional attitude, which is irritating to me since those are both things I always am), you cannot kill him here, he escapes. And if you didn't find out a secret about Madison, you can't watch him die later. You CAN, however, make him betray Leland, but that's not nearly as satisfying.
"Arrogant? No, arrogant is shooting an unarmed woman in the back and assuming that means you can take me out."
Unfortunately, if you have not done your utmost for the entire game to piss Marburg off (which means you cannot be a stealth character or a Professional, since he respects an agent who keeps a low profile and a professional attitude, which is irritating to me since those are both things I always am), you cannot kill him here, he escapes. And if you didn't find out a secret about Madison, you can't watch him die later. You CAN, however, make him betray Leland, but that's not nearly as satisfying.