In the scene after the film is finished, they show what looks like a proto-alien crawl out of the dead space jockey. For those of us (including me) who see Prometheus and the AVP films to be from the same universe, what does this mean? For me, it means that the Aliens from AVP (and maybe Alien) may not have been created by the jockeys. For those who see Prometheus to be in an alternate universe, this could very well be the birth of the xenomorph.
Though, if this were the birth of the xenomorphs, the question still remains how did the jockeys manage to not only get their hands on it, but also make it asexually reproduce by the time Alien occurred (which is only what... 50 years?) and it appeared that the proto-alien still had a lot of evolving to do; inner mouth, back protrusions, etc. Currently, I'm just seeing it as a freak mutation going on a similar evolutionary path as the original Alien from AVP (or maybe the Alien films, depending on your canon preferences).