This one is one of the easiest years for me to pick GotY, and one of the hardest to pick my favourite.
There were several games I really liked, Batman: Arkham City, Deus Ex: Human Revolution, The Legend of Zelda: Skyward Sword, Rayman Origins, The Witcher 2: Assassins of Kings, Trine 2. I was fairly certain I wouldn't care for Skyrim even before it launched, given that I already found Oblivion to be systemically inferior to Morrowind, so no surprises there - not a bad game, but ultimately TES for CoD era.
My favourite game comes down between Portal 2 and Dark Souls. Both sequels (of a sort in case of DS), both refining the formula, and both very different from each other. It's really a flip of the coin, since I can't really choose.
My vote, without a second thought or any shred of doubt, goes to Minecraft. Its influence, both on players and developers, in addition to being the best-selling game of all time, makes it once in a generation kind of thing. I personally find it to be quite good and fun, though nowhere near close as my favourites from this year.