Alien is my favorite movie of the franchise. What really pulls me into the films is the atmosphere, the designs, the sounds, the music, and the creature itself. Alien is the only movie in the franchise that actually makes me fear a lone xenomorph.
Aliens is the runner up for me. I feel the film had stronger characters and is more fun to watch because it is more action oriented. The only problem I have with Aliens is what I consider the "dumbing down" of the xenomorph. The xenomorphs are still scary and pose a great threat, but they don't match the original design of the creature. However, I don't feel it is a flaw with the films itself, so I do not mark it down for that.
Alien 3 is a film I have grown to love over the years. I feel it's a big step-down after the first two films, but I also feel the Assembly Cut has made it more worthwhile. This is just a case of bad studio interference and lack of funding. While I feel Alien 3 isn't a necessary addtion to the franchise, I feel it works well as the wrap-up to an overall great trilogy.
Alien Resurrection is a love it/hate it film for me. I like many things about the film, but I also dislike almost the same amount of things. I feel Alien Resurrection is a very unnecessary addition to an other-wise wrapped up franchise.