Street Fighter IV - 3
Flower - 2
Hook Champ (iPhone/iPod Touch) - 2
Canabalt (iPhone/iPod Touch, Web) - 2
Beat It (iPhone/iPod Touch) - 1
I would have voted for Rhythm Heaven, but I played through the Japanese release last year, so I don't think I can count it (same goes for Retro Game Challenge). Now that I think about it, a lot of the games I played this year came out last year, and I still haven't played quite a few of the 2009 games that I'm interested in. Likewise, a good many of the this years titles were delayed, otherwise I'm fairly certain ME2 would be on my list.
I voted for SFIV because I've played it so much and how consistently deep and entertaining it's been. It does scare me how little I've played compared to some gaffers though :lol. Flower was a very cool experience, and one of the few examples of motion control making total sense. Hook Champ shows how much (the very underused) mechanic of swinging can vary from game to game and how fun pure locomotion can be. Where Hook Champ felt built from the ground up with iDevices in mind, Canabalt working so well is a happy coincidence of its one button control scheme, and it's just really excellent and atmospheric. It's especially cool how although the game from moment to moment is more or less homogenous, the way the music varies in intensity and and at times drops out completely really changes your perception and focus. Finally, my remaining point goes to Beat It, which, like the previously mentioned Rhythm Heaven, shows how little the music game genre has been explored, and how Guitar Hero, Rock Band, all the Bemani games, etc. are the same goddam game and are a drop in the bucket of what can be done.
I kind of wish I represented more platforms on my list, but it is what it is. I haven't played much DS stuff recently (still want to try Scribblenauts though) and PSP hasn't had too much of interest to me either, but the day the sequel is released to Metal Gear Acid 2, the secret best PSP game of all time, is the day a game, beyond all rules of voting, will be given 10 points. I still haven't played NSMB Wii or Muramasa yet either, and Pixeljunk Shooter is sitting unplayed on my PS3 hard drive. It's impossible to keep up.