Which Game do you consider the Best FPS of the 90s?

Half-Life is the game that change the genre and have a great way to tell a story - a first person expirience.

You didn't mentioned Quake 2.

Star Wars Jedi Knight: Dark Forces II. Because it still has the best level design ever created in an FPS.

Holy thread necromancy, Batman.

Team Fortress Classic. But that's primarily because of the insanely large learning curve and game mechanics which in turn created a lot of replayability.