For me...
#1: Resident Evil 4
The pinnacle of video games as a medium in my opinion. From it's pulse-pounding action, to its perfect pacing, to its incredible boss fights, to its atmosphere and audio-visual design, it's simply a masterpiece in every way.
#2: Super Mario Galaxy
The perfect blend of insanely polished gameplay and pure childlike wonder. It's like they distilled happiness into video game form.
#3 Bioshock
A tour de force in atmosphere and storytelling, set in an unforgettable world and galvanized by its superb plasmid-powered combat.