id Software, Bungie and Rockstar.
Id pretty much revolutionized the FPS genre with games like Doom, Quake, Hexen, Heretic, Wolfenstein and Commander Keen.
Bungie was right after with the Marathon series. They also made Oni, the only game I know that really combines hand-to-hand combat with fire arms seamlessly, and it had a great plot too.
Rockstar, the developers behind the entire GTA franchise. Need I say more?
Oh, now that I think about it, Capcom, Konami, Namco and Nintendo have made some great games too...