The best picture in the series is the original; it utilized the resources available to it more efficiently than the other films in the franchise.
My favorite is Alien 3. Tonally, thematically, I feel it speaks to something intrinsic to the human condition. Its religious angle both echoes the strange Feudian spirituality that serves as a subtext in Alien and foreshadows the overt von Däniken-based religious concepts that drive Prometheus. In my mind, Alien as a series is as much about religious horror as it is body horror or jump scares.