During that decade I played pretty much every FPS that was released and Half-Life 2 is so far ahead of the competition it's not even funny.
Best graphics at the time (with Far Cry)
Best storytelling in an FPS
amazing value (~14 hours singleplayer)
impressive physics engine
varied gameplay (puzzles, shooting, driving, platforming)
interesting characters
fantastic atmosphere
iconic soundfiles (weapons and suit)
Perfect in every single way.
Runner-up is probably Bioshock.