The grand bleak architecture and raw, basic reality of the lives and location. Initially I disliked (like everyone else) killing off Hicks and Newt so unceremoniously after their being Ripley's "great success" of Aliens. But it sets the consistent, depressing tone of the film, which is maintained throughout.
I think there's a Quake aesthetic as well, which I have a pronounced soft spot for (in addition the the first person alien view aspects towards the end of the movie).
I rewatch Alien 3 one every couple of years. I still love it.
Not to mention it's got some first rate actors too.