I don't want your run of the mill War game or special ops either. It has to be atmospheric.
On your list I would say
FEAR has the most pizazz.
Ones not on your list.
The meh OK games.
Quake 4
Prey
Prey would have the better story. Quake 4 is more team based at some points.
The
Deus Ex sequel is still a good game in its own right. It plays like the first one with a more non-linear gameflow as the story progresses.
The first
Painkiller series has a lot of atmosphere but very little story and is pure action.
Dark Messiah of Might and Magic has a decent story. It is not a traditional shooter however.
Vampire Bloodlines has a great story and atmosphere but has equal roleplaying elements so that may not be what you are looking for.
The
NOLF series is great if you can find them. The same goes for
XIII.