I'd have to say either Braid, Cave Story or Portal.
Cave Story, there doesn't even really need to be much dispute over. The game is flawless is most respects, not to mention its outstanding story, beautiful sense of nostalgia, and nearly bug-free prgramming. And the fact that it's made by one person makes the feat all the more amazing.
Braid is just a beautiful accompishment. The time travel elements woven into the soothing atmosphere and gorgeous music, on top of the most genious game ending probably in the history of video games makes for an experience that only comes around once in a decade.
Portal is a relatively short game for Valve's of making long games, like Half-Life. 2 hours was all they needed however, to ensure the portal gun as one of the most innovative new leaps in technology this decade. Those two hours were also enough time to secure the Faithful Companion Cube, GLaDOS, and the cake into our hearts :)
Sorry, I could only include one picture :(