I must say that I'm surprised that no-one's mentioned Quake (the first one).
I mean yes, the original game wasn't absolutely brilliant, but with a little imagination the universe it created could be filled out to be something absolutely awesome.
I mean, look at the potential you've got here - a large human military force fighting demons, a main character who ends up wandering countless dead worlds who turns into something not quite human, an axe, zombies, and the phrase 'The Slipgate War' (come on, tell me that isn't a cool sounding name). Oh, and level names such as 'The Nameless City' and 'Province of the Abyss.'
Or maybe I'm just crazy.
Also, I would love to see an update of X-Com Apocalypse. I'm not sure if many people have played that game, but it's awesome. All of the terrain is fully destructible (in its own rather blockish way), it allows you to have agents duel wielding chainguns loaded with incendiary ammunition (causing untold damage), and you have an entire cityscape made up of various corporations with their own inter-relations. The game was brilliant and it had even more potential.
And Quake 2. And no-one's allowed to say "Oh, but that was kind of done in Quake 4," because Quake 4 was crap. I prefer Quake 2 in every single way (including graphics!! (Okay, admittedly Quake 2 suffered from never being able to fight alongside friends - that was probably the biggest downside - but all older games suffered from that affliction)).