What a year...
My top three (and they are hard to choose)
1. Mass Effect: For me, the fact that I'm playing and choosing the story really takes gaming forward. Not a perfect game, but it has some of the elements I've always wanted from games.
2. Super Mario Galaxy: A pure, fun, gaming experience. An instant classic. Their chase camera really impresses me as well.
3. Halo 3: Great battlefield AI, inverse kinematic animations. Forge, Saved films, screenshots, Bungie.net integration, the standard for console FPS controls, "gameplay first" level design...Halo innovates it many ways over scripted shooters like Bioshock and COD4.
Honorable mentions: Uncharted, Ratchet and Orange Box.
Still, any of those games could (and will) get GOTY award from all over the web and I won't be upset. COD4 is the only "contender" that I feel isn't worthy amongst the aforementioned titles.