Alien is comfortably my favourite. James Cameron's films have never really stuck with me, as such I managed to enjoy Alien 3 more than Aliens. Perhaps this is generally due to bland narratives? I'm not entirely sure. On top of what I think is an incredible movie, it might be important to note that Alien has had an enormous influence on cinema.
Prometheus had its ups and downs but overall I thought it was pretty good. The panicked operation scene was genuinely brilliant.