Far Cry 2 - the ending make no real sense whatsoever. It involves a relatively mediocre fight against the AI, to achieve an objective you don't really care about.
A close runner up would be the ending to Dragon Age: Awakenings. Don't get me wrong, I love Dragon Age and all things Dragon Age related. But the ending to Awakenings involved your character VERY AWKWARDLY walking away from the slain end boss with a bemused expression on their face. Then it just cuts to some rather lame splash screens detailing what became of who. I was in shock - literally, you kill the boss, get about 5 seconds of the boss screaming in agony, before dying, and then another 4 seconds of your character stumbling away from the dead boss with a perplexed expression on his/her face. It was just jarring.