Ridley Scott says that "Prometheus" also follows a traditional sense of the story of the titan who stole the gift of fire from the gods and gave it to mankind. If you have no idea about the story of Prometheus, I suggest you educate yourself and look it up.
That being said, here's some of my theories: I believe the Jockey is a rogue scientist/exile/perhaps even a criminal of his own species. Who essentially decided to take the "gifts" of his race's technology and exploit them upon the galaxy/universe. Perhaps creating several new species and creatures, including humans. Either he does this to get back at his kind or like an outcast scientist wanted the freedom to explore without moral constraints.
Following that trend, it's quite possible that the Jockey even "befriends" the humans who discover him. Allowing them to study his technology even though he possibly knows it will corrupt and mutate them (hence the "human mutations"). Much like the titan Prometheus, the Jockey was outcast from his own race and now wants to use his technology AGAINST his own people, perhaps even destroy them. Ultimately, the experiments and such go wrong, everything then culminates with what he believes will be his "perfect species/warrior", the Xenomorphs. And we know how that goes...
However, the movie displays a lot of the "exploratory" theme and the Jockey might be an "unseen force/observer" until the end of the movie. He ALLOWS the humans to take his experiments/technology/etc., because he wants to see how the bio-experiments/technology will affect them. Perhaps all with the motive to create a "warrior species" much like my other theories. Originally, the bio-junk, whatever may mutate them into the warriors he needs/wants/or just plainly observes to see what happens.
The ultimate mutation however, might be the Alien Egg. For those who remember the "cut" scenes from ALIEN. Ripley discovers Dallas in the ship stuck to a wall slowly "mutating" into an Alien Egg. Ridley Scott has said that was how the Aliens "bred" at the time. Now, granted James Cameron changed that by introducing the Alien Queen, but in the absence of a Queen, even ants have ways of "creating" one in order to propagate their numbers.
When you drink whiskey whilst typing it becomes LV128!
