I prefer Alien, but as others have said; they're two different movies so it's hard to compare in many respects.
I like the more basic approach to the first film, few characters and just one, horrid thing in the darkness. The second film is amazing, relentless ride, but it doesn't have the same horrific quality as the original (which I, personally prefer).
Oddly enough I had a freaky dream about Alien last night - Veronica Cartwright was doing her squirmy, afraid face in a corner and the xenomorph was advancing ridiculously slowly. Also had a weird Aliens inspired one a while back, but that occupied the more... downright ridiculous dreamworld, lol.