It's funny how any of the *really* good games released in the last few months and the coming months could easily win GotY any other year. Think of all the games not even being considered:
Halo 3
Rock Band
Uncharted
Metroid Prime 3
Zack & Wiki
CoD4
Ratchet and Clank
Assassin's Creed
Guitar Hero 3
Phantom Hourglass (how awesome would it be for a handheld game to win GotY)
RE4: Wii (possibly)
UT3
Portal
TF2
and I'm sure there are others I'm missing. It's just amazing the year of games we've had and the insane competition this year.
Personally, I'm thinking it's going to be a tough race between these three games:
Bioshock - I don't think the fact it's fading in people's memories is going to affect too much. It's a game that did an absolutely incredible job of placing the player in a place that felt so real (best I've ever experienced) and it told a wonderful story. The only negative was the basic gameplay and I think that's why it isn't going to win GotY.
Mass Effect - Even though it hasn't been released yet I'm still expecting a lot from this game, though like Shams this could be its downfall. With a game that does so much it's so easy for it to fail at one of those many things (even while succeeding so well on everything else) and stick out in peoples head. It's kind of like a jack of all trades-- it could be a master of none.
Super Mario Galaxy - I'm fairly sure this is going to be the Game of the Year. It has all the great things about Mario64, improves on things that were wrong in previous Mario games, adds new gameplay to the already impressive series, and completely rejuvenates the platformer genre. This is a pretty ambitious game and from everything I've heard it has pulled everything off beautifully.