For me this has to be one of the greatest games ever made. It combines claustrophobic survival action, great storytelling and cyberpunk thematics, puzzle solving, solid character development system, and above all, just unparalleled atmosphere.
You really were blown away back then (and I'd say still today) the first time you rigged an alarm and a pack of mutant zombies made a rush for you in the narrow hallways, and a kick ass cyberpunk techno song began blasting through your speakers! Man this game was intense. You never knew when you were safe, when your gun would jam or when you would run out of bullets (ok - eventually you'd get better, but this game was at it's best with a high difficulty / high intensity playing mentality. And high music volume!).
The details of the story might not be that revolutionary, yes we have seen this before. The flesh versus machine, the theme of dehumanization. It's not in the story or the themes, it's in the delivery. We see gruesome images, we listen to audio logs that really spark emotions in us, that really seem to tell stories of their own, not just some quickly made up sidequest stuff like in so many other games. These contain real feeling. The player lives with the story, and ascends deeper and deeper to the final confrontation.
Bioshock, although hugely popular, was just a shallow copy of this game. Same story structure, weaker story themes, weaker characters (shodan vs .. who? I forgot the name of the villain in bioshock), much lamer music and surprisingly, a weaker, simplified character development coupled with simpler level design and tuned down puzzle difficulty.