Maybe not best (such a heavy word), but my favourites:
SW: Dark Forces (1995)
Quake II (1997)
Half-Life (1998)
ST Voyager: Elite Force (2000)
The Operative: No One Lives Forever (2000)
Return to Castle Wolfenstein (2001)
Vietcong (2003)
Far Cry (2004)
The Chronicles of Riddick: Escape from Butcher Bay (2004)