Yeah, the games Valve crafted with Half-Life and Half-Life 2 are just utterly legendary. Especially HL1. The mods that game spawned were ludicrous. Counter Strike gets all the rep but Day of Defeat was even better. I think I poured thousands of hours into them total. The single player portion of the game was so chock full of atmosphere and details (for that time), seemed like around every corner there was some new terror to face.
I'm having a hard time thinking of other truly great FPS games. I do think the original Halo has to be up there. For their times, Goldeneye and Perfect Dark, obviously, but they don't withstand the test of time like Halo and Half Life. I mentioned Tribes. In terms of online/multiplayer components (that game was pretty much online-only with up to 120 players) that had to be one of the coolest, most competitive FPS titles. It's too bad the follow ups didn't live up to the original.
We live in a day and age where the FPS genre just doesn't do it in terms of AAA titles anymore and it has given way to hybrids like Deus Ex (the third installment comes out in about 6 months and looks better than ever) and Bioshock.