Two big notables for me would be Half-Life and Deus Ex.
Half-Life for it's introduction of narrative into FPS games and including characters which weren't just there to be blown up. For the first time a game's story wasn't just the bits you read in the manual or on the loading screens but something you were actually a part of.
Deus Ex for bringing hub based, narrative driven gameplay into the FPS genre where you were also free to determine your own path through the game. Not the first game to ever have a decision/consequence morality system but it sure did it properly.









