I have to give it to Alien 3. Directors cut preferred. In my opinion, from a narrative standpoint it's the darkest in the franchise. Ripley survived all of what happened in the first 2 films, discovered a new family, then had it all torn from her. As if that wasn't enough, she's surrounded by violent convicts and another alien on a cesspit of a planet. Finds one last shot with Clemens, and boom. Then the Queen embryo inside, meaning the Alien has finally gotten her. It's just a very hostile and unforgiving film. It's a shame that it turned out to be such a bad experience for Fincher, and that he will most likely never come near the franchise again, as the man is truly talented and his style lends itself well to this particular universe.
On a related subject, I wish we could have seen what a Tony Scott Alien film would've been like. That "Man On Fire/Max Payne 3" style of his would've been wild.