I'm going to second Deus Ex. Last time I replayed bloodlines, on the mission where you have to destroy the museum paintings, I was thinking over how to get inside. You could knock the guard out, trick him, sneak past him, pick the main door... and then I noticed that, if your strength is high enough, you can break through the fence. I was all happy about all this options, and then I realized it was exactly the same feeling as when I replay Deux Ex. I dare say Bloodlines is the game closest to DX that I know of, and that's high praise coming from me.

My view of the progression is something like this;

System Shock 2 - Deus Ex - No One Lives Forever - Farcry - Bloodlines - Human Revolution

None are really like Bloodlines, but the gameplay is. I wait for Deus Ex 4 to put on the end of that list.