I'm honestly not sure what my favourite is. This has been the best year for games for a while, best since 2007 at least.
Portal 2 was incredibly funny, smart and well written. Undoubtly the best story for this year, and possibly the best art design. The co-op was great and the puzzles were a lot of the fun, the only down side being that it might be too easy. But I just can't forget the best ending to a game EVAR!
Arkham City blew me away completely. The combat is some of the best combat I've ever experienced in a game, hands down. The story was really well told too, and there were just so many "holy shit!" moments, especially the villain surprises. As a comic book nut it was a dream come true, now all we need is Rocksteady to get their arse on that Superman game. This game blew my mind, now all I can think is Batman.
And I'm playing Skyrim right now and I've probably played as much as both the other 2 games combined and I still haven't even brushed the surface. This game is incredible. This is coming from someone who has problems with Fallout 3 and loathed Oblivion, this game is just so, so good! The world is fansinating (unlike Oblivions fantasy world 101), the exploration is fantastic, the character leveling system is the best I have ever seen in an RPG. With a game this large there are little problems; combat isn't brilliant and there are other niggerling problems like bugs and the still odd looking people. But with a game this big it's hard to hold much against it, and more than any game I have played in a very long time it's worth every single penny. I will say that this is a much, much slower paced game than anything else I've played this year; there are very few blow mind moments like Portal 2 or Arkham City, but I kind of like the change of pace.
As far as indie goes I'd also give a shout out to Bastion, which was a beautiful bit of story telling in the way only a game can and From Dust, which despite it's problems captured my heart just because of weird it was and the nostalgia for Black & White I got.
But I can't choose one game, and there's still so many I haven't bought (Uncharted 3, AC:R and Skyford Sword chief amoung them)