I'll skip the obvious ones and mention a few boss games that you probably haven't played, from this year.
Blur - Racing game somewhere in between Mario Kart and Need For Speed, by Bizarre Creations; a Liverpool-based studio. It sold poorly, but was an awesome game. The online is by far the most fun I've ever had with any racer.
Enslaved - Masterful storytelling, via the medium of games, with mo-cap and voice over by Andy Serkis. Gorgeous game.
NIER - Not for everyone, but it's just a lot of fun, and has probably the most interesting and heartfelt story in a Japanese videogame... well, ever, for me. It's never boring either as the game shifts into a crazy amount of styles. It's mainly an action RPG, but then one minute it's a top down shooter, then a Harvest moon-esque farm sim, then there's the resident evil mansion bit... This is probably my nomination for the best game of the year that didn't sell very well.
Ilomilo - Just got this puzzle game the other day for the 360's xbox live arcade, and it's an amazing looking game, with some real mind-bending, innovative puzzles. Well worth the 800msp (£7ish). Do buy it if you can!
My favourite game of the year, which did sell well, was Mass Effect 2. And that's probably my game of the decade, too.