Metal Gear Solid 2, for making me play as Raiden the entire game, instead of...say, a character who isn't amazingly lame. The general incomprehensibility (with the fact that it's a Hideo Kojima game in mind) of the plot counts as well;
Deus Ex: Invisible War, for tarnishing one of, if not the, best RPG/FPS hybrid games to ever exist;
Every game post-DOOM (and a few before, perhaps) with GRIZZLED SPACE MARINES, who are apparently now the industry standard for FPS games (and other genres!) set after the year 2012;
Final Fantasy 7, for making angsty, whiny main characters the new face of JRPGS;
Kingdom Hearts, for thinking Disney characters plus Final Fantasy would equal anything other than an odd-to-watch wank of a game that came off as little more than bad fanfiction, as well as spawning a legion of FUCKING OBNOXIOUS FANGIRLS DEAR DICKTITS I WANT TO MURDER THEM ALL; (At least the game engine was solid.)
Microsoft, for introducing this "Microsoft Point" nonsense that makes me physically ill, as well as gamerscores, most of which boil down to doing boring, nonsensical things in multiplayer that have nothing to do with crazy things like playing the goddamn game;
Several game companies/producers/what-have-you, for releasing DLC and half-finished games that they charge you to finish up. Bonus points if said DLC is incremental and takes the place of a proper expansion pack while costing twice as much;
And most of all, quicktime events.
I'm sure I missed a few things, but these are the gripes that came to mind pretty quickly.