Indigo Prophecy, Shadow of the Colossus/ICO, Call of Cthulhu: Dark Corners of the Earth, X-Com: terror From the Deep, Indiana Jones and the Fate of Atlantis, any Tim Schaffer game (Grim Fandango, Day of the Tentacle, Full Throttle, Psychonauts), Skies of Arcadia, Valkyria Chronicles, Half Life 2, KOTOR 1, Star Wars: The Force Unleashed (say what you will, but this was a well written script that captured the original spirit of the trilogy), System Shock 2, Bioshock, Final Fantasy V, VI and VII, Resident Evil 4, MGS 1 and 3, The Darkness (except the final chapter), Fallout 3, Manhunt (very enjoyable story), I'm sure there's a ton I'm forgetting.