Killzone 2 had some of the best map design I've ever seen in an FPS - Corinth Crossing, Blood Gracht, Radec Academy, Tharsis Depot, and Pyrrhus all left a big impression on me with their multiple pathways and strategically placed turrets/ammo crates.
Counter-Strike was ahead of its time, pioneering the modern FPS with its winding urban hallways. Some of my favorites are cs_office, de_cbble, cs_estate, the dozens of community maps whose names I can't remember and that's not even getting into dust, its successor, and numerous progeny.
Call of Duty ran with that template and has had unbelievable ones - Crash, Backlot, Terminal, Favela, Estate, Afghan, Sub Base, Lockdown, Downturn, Resistance, it's insane what they can crank out over there. Ghosts has some of the best maps yet, with Tremor, Octane, Freight, Chasm, and Warhawk standing out for me.
I'm really looking forward to Epic's upcoming reboot of Unreal. Some of my favorites in UTIII were Shangri La, Heat Ray, Sanctuary, and the remakes of Deck and Facing Worlds.