Gotta be Pripyat in Call of Pripyat, it's maybe a bit too empty, but that adds to the atmosphere to some extent. That's something I actually really appreciate about CoP, it doesn't feel the need to throw enemies at you nearly everywhere you go, it's content to just let you wander around a pretty much empty factory complex and jump at shadows.

Limansk from Clear Sky I like conceptually, but the actual level in-game is mostly a linear shooting gallery, unfortunately. But still, I'm just a sucker for exploring decaying urban environments