If you turn off the rather annoying soundtrack for both Quake and Quake 2 there's lots of ambient to be heard.

Silent Hill 1 and 2, probably more in this series... Creepy through the roof!

And... Alien Isolation, ALL about ambiant sounds...

Sacred 2 had some pretty nice sounds to go along with the pleasing visuals. I thought Amnesia; The Dark Descent was decent in the sound department too. As mentioned already, Skyrim and the Witcher games are really good. Dead Space 1 and 2 were good too if I remember right.

Shadow of the colosus, awesome game.

Just wanted to second koima57's suggestion: Alien Isolation! This game is all about sounds and noises. PCGamer even had an article about the game's sound.

My god, those games had some of the weirdest / creepiest sounds ever!

IIRC Hexen had some great ambience. And the music sort of melted together with it. Turned out really atmospheric

The first two Thief games have most excellent ambiance.

So does the Stalker series (S.T.A.L.K.E.R. COP), in particular Call of Pripyat (since it's the one I've played the most and thus remember the ambient sounds well). With the sounds of distant 'things' happening, and the sounds of the anomalies, and just the crickets in the bushes; the weather - it has really nice ambient sounds.

Ah, that's why you're wearing a hard hat! Is that the very brick of depression in your avatar's pic? ;)

Dead space, amnesia, dear esther and skyrim