What, no Quake?
I voted Deus Ex, and would have done no matter what, but Quake is badass. First truly 3D FPS, first one designed to support mod-makers from the outset. And hella fun. And the engine that spawned a thousand games (Hexen, Heretic, Team Fortress, Sin, Wolfenstein, CoD, CoD 2, CoD 4, CoD:MW, Half-Life, HL2, Portal and Doom 3 to name but a few). And it's now free software (GPL), which gets Brownie points in my book.
Unreal did well too, being the engine behind Deus Ex, R6:Vegas, Gears of War, Bioshock, Borderlands, Arkham Asylum, Splinter Cell and Mass Effect.