1. Q: Is the black goo different than the green goo?
Yes, the black goo is different from the green goo. The black goo is a weapon, the green goo is a part of the interfaces for the engineer's technology.
2. Q: Is the black goo intended as a weapon, or is it just alien jizz?
The black goo is intended as a weapon.
3. Q:Why did Ridley Scott let his 3 year old do the makeup for Peter Weyland?
Yeah, the makeup wasn't great, but that's not really a plot point.
4. Q: How did Weyland know where to look (where the scientists were sitting) when recording his hologram message?
Maybe they just stuck the scientists where he happened to be looking. there's about 1,000,000 for this one.
5. Q: Why did Holloway take his helmet off just because there was oxygen? What about space disease, etc.?
To answer this, you have to look at the personality of Holloway. One answer - he had faith in the engineers, and didn't believe that there would be "space infections" in a place they had terraformed.
6. Q: Why did the biologist run away from the dead engineer instead of trying to study it?
He had just had first contact with a dead alien. He was a little freaked out. Is it entirely believable? maybe not, but it's not THAT far-fetched.
8. Q: Then, why did the biologist try to play with the weird space penis'?
Lets not forget he was really fucking high at the time.
9. Q: What was the point of revealing that Vickers was Weyland's daughter?
It's a plot twist. Its purpose is to make the movie more interesting.
10. Q: Why did David give Holloway the black goo? Is he just evil, or what?
David gives Holloway the black goo as an experiment - he wants to see what will happen, in the pursuit of trying to discover immortality for Weyland.
11. Q: The black goo turned mohawk dude into a raving zombie, so why did it cause a black worm thing to wiggle in Holloway's eye instead?
Just some sort of side effect, or part of the transformation - the black goo seems to cause everything to mutate differently.
12. Q: Did David know Holloway was going to have sex with Shaw, and create a monster alien squid baby?
No, he didn't. That just happened, and he took advantage of it when it did.
13. Q: If the engineers created life on earth, why do animals not have the same DNA as engineers, like humans?
Do they not?
14. Q: If the engineers created life on earth, why were there 60 million years of dinosaurs before humans?
Why can't "created life on earth" not mean evolution still took place? It doesn't say that they created humans out of thin air. They basically gave the earth DNA, which allowed things to evolve.
15. Q: Instead of chasing Shaw and Vickers, why didn't the engineer just fly away to destroy earth?
He couldn't have flown away - The ship crashed. He was probably pretty angry and wanted to fuck shit up, so came looking to kill Elizabeth.
*16. Q: How did Mohawk-dude and the Biologist get lost when the ship has a 3D map, and their in constant communication with the ship?
Because the people at the ship didn't even know that they had split off from the group and gotten lost until the storm hit. By then, the 2 scientists had to wait out the storm anyway.
17. Q: Why would the majority of the scientists go on a mission without knowing its purpose? What if the mission involved a gang-bang?
For the money. If you've seen "Alien" or "Aliens", you already know that the Company doesn't tell people shit.
18. Q: Why did Weyland preteen to be dead?
So that nobody would know the real reason for the trip. This left him free to do things like have David infect Holloway.
19. Q: Why did the engineers leave message that pointed to one of their military installation worlds?
This is open to interpretation - There is no obvious answer, but it is possible to come up with plenty of reasons why they would choose to do this.
20. Q: Why does no-one seem to care that Weyland is suddenly revealed to be alive? Why don't they seem to care when he dies?
When he is discovered to be alive, shit has already hit the fan. She had just aborted a SQUID BABY. Things just didn't seem as weird after that. When he dies, everybody is frantically trying to survive. They don't have the time to care that he died.
21. Q: Why did Shaw and Vickers try to run away from a rolling circle ship, instead of to the side?
From where they were, it wouldn't be as obvious to them as to the audience that it is a rolling circle ship. They are just trying to get away from it.
22. Q: Why did the engineers decide to try and kill us, when they were the ones who created us?
The most popular interpretation here is that it is because we crucified Jesus, who was an engineer.
23. Q: What's up with the "security footage" of running engineers?
They were presumably running from some sort of outbreak of the black goo - possibly mutated engineers.
24. Q: If the engineers were trying to escape an outbreak of the black goo, why would the one who got beheaded try to go into the black goo chamber?
Some people say that he was just committing suicide, or praying to the mural on the wall, or the giant stone head, or something like that.
25. Q: What is Prometheus?
Prometheus is the name of the ship they take to LV223.