Brigador and Ember have a fixed camera perspective though, haven't they? So they feel more like isometric games, even if they run on 3D engines. I can't claim to know what the OP is looking for exactly, but I think the games she listed all have more or less free camera control in the 3D world.

Legacy of Kain: Soul Reaver

and though it's not really in line with those you mentioned:

F.E.A.R.

Mount & Blade series is on sale now.

Freespace 1 and 2, though a joystick is all-but-required

I-War2, also joystick requirement

Wolfenstein 3d and Doom

Hard to think of any as there are not that many 3D games around...

Rune hasn't been mentioned yet.

I've just finished Indiana Jones and the Infernal Machine and it's really good. Think of early Tomb Raider but with more focus on puzzles and more clunky fighting segments (there are planty of health packs around so it shouldn't be a problem though). I've played it without any nostalgia factor and enjoyed it a lot so I can wholeheartedly recommend it!

Deus Ex?
What do you mean by 3d exactly? Do you mean not a 2d side scroller / platformer? Because if so, there are like, thousands of possibilities.

Mirror's Edge.