Alien got an R rating mostly for scenes of intense sci-fi violence, which is apparently a different flavor of violence than your everyday violence in the eyes of the MPAA.
For example, at one point an alien baby graphically bursts its way out of a man's ribcage. It is one of the most disturbing man-gives-birth scenes in the history of cinema, second only to Junior.
Arnold's birth-face still haunts our darkest nightmares.
Since the crew of the Nostromo is a bunch of blue collar space workers, f-bombs and curse words are dropped all over the place like crew member body parts once the alien gets a hold of them. To be fair, it's pretty subdued, especially considering the language of R movies these days.
Finally, in one scene, Ash attempts to murder Ripley in a room with some soft-core porn pictures taped to the wall. Unless you're deliberately looking at the background for Easter eggs, you probably won't even notice. But since your brain will subconsciously take note of it, we thought we'd give you a heads up.