The Mark of the Ninja http://www.gog.com/game/mark_of_the_...pecial_edition . Don't dismiss it because it is 2D, as far as stealth games go it really is brilliant, the stealth mechanics work perfectly and it looks amazing, so much fun to play.

Also just started playing SCP Containment Breach which is free http://www.scpcbgame.com/ which seems pretty atmospheric...but yeah only just started this.