The ones where your leader betrays you, and the amnesia ones that totally make sense (Better amnesia games are to make you think "WHAT THE HELL?!") HEavy Rain seemed more like a movie than a game, and all the endings were the same, like Yahtzee pointed out. Halo 2's plot pissed me off, everyone was too goddamn derpy to just figure out "LET'S NUKE THE SHIT OUT OF THEM!!!!!" Also, generic terrorist organizations (Modern Warfare and Bad Company). Russians hate you for no apparent reason, except for the fact that they're Russian and that they're all assholes (in video-games)
Kingdom HEarts' plot makes you trip balls