Hard to say. The GotY would have to just surpass ALL expectations and just be great enough to eclipse any negative criticism directed towards it.
There are a lot of games that fit this category. Mass Effect 2 and Starcraft 2 certainly fit this. Limbo came and blew away all expectations for a standalone (not a sequel) and Heavy Rain just seems like an overly thought out cutscene story (but to be fair, I haven't played it).
But my vote would be Minecraft. Coming in out of left field, this was the year Minecraft spread like a virus among the gaming community.