Prometheus/Fridge

Fridge Brilliance

The Prometheus is taken out by a Heroic Sacrifice: ramming itself into the Space Jockey ship and creating a massive explosion. Prometheus gave fire back to the gods, with interest.
The unusual, overly predatory, and even self destructive nature of the iconic Xenomorphs is finally explained. They never evolved in the wild through evolution but were engineered by the space jockeys as a perfect WMD. They can spawn from a single egg or possibly even a few cells. They rapidly gain momentum once people are being infected. They instill paralyzing terror. They keep going until they run out of things to kill. And once the planet is purged of all life and the active Xenomorphs starve to death, the eggs stay behind for thousands of years making sure the few survivors can't repopulate. And on top of that, the engineers have an arsenal of other biological nasties at the ready in case all of this wasn't enough.
The Engineer at the beginning is Prometheus... or at least a metaphorical representation of Prometheus; a wayward "god" who created a new sentient species, possibly against the wishes of the other "gods" who intend to correct his mistake.
No wonder "The Mountains of Madness" film has been put on permanent hold. The Engineers are the Elder Things and the black sludge are shoggoths!
The Black Liquid in this film also gives an answer as to another mystery of the Alien Universe. Namely the deleted scene in the first Alien Movie where a lone Xenomorph was shown to be mutating captured crewmen into either eggs or new Xenomorphs. This makes a HELL of a lot more sense given the fact that we now know the Xenomorph was almost certainly created using the Black Liquid Mutagen, and may well be able to replicate it's properties to some degree in order to spread.
When Shaw tries to use the pod in Vicker's chamber to abort the alien fetus growing inside her, it says that it is programmed only for male surgeries. One may briefly wonder why Vickers would have a male pod, until you realize that her aging, sickly father is also on the ship, and may need some emergency medical assistance when he comes out of cryo-sleep.
The weird little glance down Vickers does when the hologram of Weyland mentions how David is like the son he never had makes more sense once you find out that she's his daughter.
If any knowledge of the Engineers' language ever got back to Weyland(-Yutani), there is now a plausible explanation for Mother deciphering the distress call in Alien.

Fridge Logic

If the Space Jockeys started life (not humans but life itself) on earth--why would there be cavepaintings of a star map some billion years later?
- The film implies they (or at least one) stuck around for a bit before leaving, "engineering" human civilisation: maybe they waited for it to hit a certain point, then left, giving them the codes to follow along. Failing that, maybe they left and came back for a visit, as hypothesised in the below answers.
Why would they later visit Earth and paint a star map--if they just wanted to destroy life on Earth?
- Maybe only a few, or maybe just one, wanted humans to evolve whilst the others were against it.
- Maybe they saw how far their "offspring" had come and felt threatened. Like the titan Cronos eating his children.
  - In that case, the star-map might serve as a test: if humans were advanced enough to reach the planet, they were advanced enough to be a threat and be destroyed.
- Maybe they saw humans as an abomination or twisted mockery of themselves after having evolved on a different world from the Engineers' genetic code.
- Maybe they're naturally arrogant, cruel, and warlike; "human nature" is often accused of being that way and we did come from them...
- Maybe they wanted to pit their best creations (humans and xenomorphs) against each other.
- Maybe they are just Dicks
- Maybe the Engineers have different factions, and biological warfare is just how they roll. Earth was the weapon of one group and the Xenomorphs a more advanced weapon used to target Earth by another group.
Why would they need exremely dangerous biological and chemical weapons to destroy life on Earth? They could easily make do with something that only posed a threat to humans--and not to themselves too.
- Not very easy, since we're more or less biologically identical to them down to the genetic level.
If they wanted to kill all humans--why didn't they do it while people were cavemen and a without means to defend themselves? Why wait?
- It's established in the movie that the Engineers/Space Jockeys were all in their equivalent of Hyper-Sleep if they weren't dead. I don't remember if it mentioned how long ago the holograms were recorded but they may have been killed or forced to sleep, but they may have been in such a state since shortly after humans evolved. Waiting for something to wake them...
Why did David infect the crew in the first place? He's smart enough to know it's probably dangerous, and I doubt he was ordered to poison his own team, what with the boss being on board the ship too.
- Partly because he doesn't like Holloway due to being enamoured by Shaw but also because he was testing the life preserving qualities of the liquid so that it might benefit Weyland which was his true purpose on the ship.
- Possibly because he was simply curious as to what would happen. He did sort of sneakily ask Holloway's permission before infecting him, but his moral ethics concerning Holloway's health and safety didn't really extend beyond that. Given his comments to Shaw regarding Weyland, his concern for his "father's" safety is unlikely to be very great either.
- For all we know, he said something incredibly provocative to the engineer instead of what Weyland wanted him to say. Hell, it's possible David was beyond anyone's control from the very beginning and he was just doing stuff out of curiosity the whole time. Curiosity seems to be his one defining emotion since he was constantly studying during the trip from Earth.
How did the giant facehugger actually grow to that size? When we last saw it, it was the size of an infant, so where did it get enough food to grow that big if it was locked in that sterile room?
- The typical form of the Xenomorphs was probably created by chance. The mutagen warps living things and even spawns them on its own, but you never know what the resulting monstrosity will look like in advance. The only thing you can be sure off is that it will try to kill you or wants to impregnate you. Probably both.
- Due to the nature of the machine it might have had blood for transfusions. The facehugger might have even been able to use the drugs or even anything else in the room as food.
If the Engineer specifically created human life on earth, then why are human cells so similar to plant live already existing on Earth? Also, if there were animals already living on Earth, why is their biology structure so similar to that of the Space Jockeys if they evolved on separate planets?
- Ridley Scott's stated that that Engineer at the beginning started all life. This creates problems of its own, of course.
  - He may have meant all life on Earth.
Why did the Engineers speak Proto-Indo-European? That's pretty implausible. Rather marked linguistic change over a short period of time is well-attested in history--just look at how many languages Latin developed into over the course of a much shorter timespan than the thirty-five millennia from the era of the Scottish cave painting. Proto-Indo-European is believed to have been spoken much later than that; current estimates place it at about a tenth as far back as the cave painting.
Just how did the Engineer survive that long anyway, it's clearly been shown that facehuggers can breach hypersleep chambers. More over, why did he immediately set the ship to take off? Wouldn't it make more sense to...i don't know check the ship to make sure the things that murdered everyone in it were really dead, or at least make sure the new arrivals didn't trigger a new outbreak. Lastly how did he know they were from earth? All he could tell in the few seconds before he started killing was that they weren't Engineer's.