My first proper introduction to FPSers was Marathon on the Mac and played its sequel Durandal almost religiously, so while I may not be much of a Halo fan, Marathon 2 always holds a special place in my heart.
On the console side, the only FPS I ever really liked or thought was well-done was Maken X on the Dreamcast. Metroid Prime 2 is a good game as well, but more in terms of atmosphere and feel than in actual gameplay. Maken X had the best of both worlds, it had a solid engine, a respectable story, and a great presentation.