My favorite is Alien. I honestly rate them like this.
Alien
Alien 3
Aliens
(and way, way down there,) Alien Resurrection
Alien is my all-time favorite of the Alien (solo) films. It's truly the best one out of the bunch, and it works on every level it sets out to work upon. Alien 3 comes next because it is the one sequel that managed to actually feel like an honest-to-God sequel to Alien. Aliens is damn close to Alien 3, but the only thing that brings it back a little bit is that if you basically took out all the Alien aspects of the design and replaced them with random creatures, and took out all references to the first film, it could stand up as it's own movie, totally seperate from the rest of them. In other words, it felt a little more like a film that happened to be about Aliens, rather than an Alien film. A word about Aliens in a moment. Resurrection, well, I don't need to say anything about that. I don't despise it with every inch of my soul, but it's really below the rest of them.
Now, my word about Aliens. I may get a lot of crap for this, but I think Aliens is the most over-rated film of the series, and not only that, but it's strange how over-rated it is when you consider how different it was, and how much it changed. I always laugh when I read people whining about AvPR's little deviations and alterations, yet people cheer for the ones made in Aliens. Why? Because Aliens was only the second film. It was not a franchise yet. No one cared if Cameron literally f**ked with the design of the creatures, or added in things that never existed prior, or turned them all into bugs, and still, no one cares now. It came out during a period where actiony films of it's kind were PRAISED as HOLY, and at that kind of film, it is very successful, and I think that had a part to play. Those kinds of films were in when it came out. Also, the mystery. Where the mystery of the Alien in the first one was very, very high, it was smashed to pieces, and now the only real mystery left to them is what the Space Jockey's are.
Don't get me wrong, Aliens is a great film, and I'm always quick to watch it even if it's only half-way through, but still, I think it gets much more praise than it should.