My GOTY is Fallout 3. Though it is technically a 2008 title, I didn't start playing it until very late last year. But shortly after I started, my Xbox died and I was unable to play. So, I didn't really play the game at all until this year. And going by time spent playing, Fallout is easily my most-played. I've played through the game 4 times now, all the various DLCs, and every quest. It is a fantastic game.
But, if it has to be a game from 2009, then my GOTY is Halo 3: ODST. I'm a big Halo fan, and even though this game was not quite what a lot of people wanted, I have a lot of fun playing it. The campaign is very fun and different from previous games, and Firefight is a blast with 4 people. It was the perfect game to tide me over until Reach.
My runner-up for 2009 would be PixelJunk Shooter. This just recently came out, but it is AWESOME. I love all of the PixelJunk games, and this one is no exception. The control is fantastic, I love the art style, the music is great as always for PixelJunk games, and it is very challenging without being overly hard. It is a little short, but the probability for an "Encore" expansion is almost guaranteed. Highly recommended for PS3 owners.