Longshanks said:
Blade Runner (great atmosphere, good story, even decent C&C)
I feel like Blade Runner deserves special mention here. It's really an amazing game, although very different from the LA style.
A detective story at its core, it revolves around gathering clues to piece together a larger puzzle. There are multiple ways to get a clue, and often multiple ways to handle a situation. Most notably, the way you treat NPCs affects their disposition towards you and may alter the course of the story lateron. Talk about C&C. There's something like 12 different endings, not all of which are reachable in the same playthrough due to an element of randomness.
Highly recommended to any adventure fan, even if it doesn't quite fit the topic title.