Overall, I'd probably have to say System Shock 2 is my favorite PC game (and definitely is in the running for my favorite game ever). The atmosphere is just perfect, and while the combat itself isn't the greatest, the RPG elements make the game very engrossing and even helps with the replay value (it's different going through it as, say, a psi user rather than gun-toting marine). It was just extremely well executed and a great premise, and even playing through it today is still extremely fun even when I know what's going to happen.
Although...I'd have to say that the multiplayer-online
Natural Selection mod for Half-life is a very close second. Strangely enough, it has a setting similar to System Shock 2's, but I've probably sunk more hours into that game than any other. For almost a year, I played the game almost exclusively with other games only being a distraction before I came back to it. It was the first (and last, come to think of it) online game that I really got involved in, and it helps that I had a familiar server that always had players I knew on it. Unfortunately, the server and regulars kinda disbanded, and I haven't been able to get into the game like I used to be. But for the time I was into it, I really had a game I could connect to.
Jam it back in, in the dark.