Stalker and Bioshock get my votes, both had big balls and tried something new, mostly stalker though as Bio took a lot from their previous game System Shock.
It was a really great year for games for all platforms. Hopefully larger companies will be willing to take chances again like they did in the 80's and early 90's.
I mean the above games could all use a refit and rebuild in 2008 and beyond. Hell Space Rangers 2 almost brought back StarControl and Starflight in a way.
More risk, but sensible risks.
have to admit I am so fucking tired of shooters. Everything must die....YAWN.