A lot of people are saying Shadow of the Colossus, and I have to agree. There's a big difference between game of the year and game of the decade. Game of the year is short-sighted, what you had the most fun with lately.
Game of the decade is covering such a long period of time, it really has to have some depth, uniqueness, and timelessness about it. You can't just throw a game like Modern Warfare on there because it isn't as timeless. Sure, it's fun, but in a couple years they make another that tweaks the controls and make it a bit better. A decade from now, it will age, just as Golden Eye has. Shadow isn't a genre game though, it stands alone and does what it does best. They didn't come out with Shadow 2 and make it a bit better, it's still just as good as it was 6 years ago.
You want something that you'll remember and come back to and it will still be great, not that fun but forgettable time you had last year.
Shadow of the Colossus wins it for me, that's the one I choose, but honorable mentions include:
Silent Hill 2
Portal
Zelda: Windwaker
Bioshock
Final Fantasy X
Each of those I feel have aged very well and will continue to be considered great in another 10 years. I did list them in order of how close they came into consideration of GOTD for me. I think games with strong atmosphere, story-telling, and uniqueness age the best, and GOTD really depends on longevity. I also say it really needs an experience that can't be done through another medium, and really, if you didn't take down those beasts yourself, it wouldn't be the same. A book wouldn't work for Shadow. A movie of SH2 wouldn't be as scary as you playing through. That's part of why FFX was lowest, because although I love it, it doesn't rely on the medium of videogame as heavily as the others.