Doom 1 and 2, Tomb raider...full of great levels. I couldnt name a specific one but I wish they still made them like that. Hitman is a good one too, I agree.
The greatest thing for me about old FPS were the levels chock full of secrets.
That Hitman level is great done both ways: first the sneaky way, then, once you've unlocked all the weapons, go back and slaughter every gimp on that dance floor. The music just makes it that much more satisfying.
http://www.youtube.com/watch?v=V_z7AZR2euo. Its not so much the level itself as it is that....thing. The best part was that if you knew what you were doing, you could kill it.