Elizabeth Shaw, in the scene where she finds out that the MedPod doesn't do C-sections, and promptly figures out how to get it to take the Thing out of her body. While coming out of sedation an unknown amount of time ago, in terrible pain, and just barely managing to hold off panic.
The fact that she managed to run around so much afterward. If you're a woman who'd had a Ceasarean or hysterectomy, you were probably curling up in sympathetic horror with her.
Janek, Chance and Ravel's Heroic Sacrifice to stop the Engineer from leaving the planet by ramming Prometheus into its ship. Made even more awesome when Janek orders Chance and Ravel to get on the lifeboat but they turn him down and go down with the ship. The way they choose to embrace it is also pretty awesome:
Janek:Hands up! *All three put their hands up as if they were on a roller coaster*
There may be a practical reason for that- keep the hands off the controls to avoid a reflexive, if futile, attempt to steer away at the last second. Still Awesome though.
Seeing the Xenomorph prototype climb out of the dead engineer, hiss, and extend its crude inner jaws, possibly becoming the very first Alien ever created, and setting the stage for all the terror that's to come in the subsequent films.
The reprise of the triumphant main theme as Shaw decides to go to the Engineer homeworld. It's like a triumph of the human spirit against all odds, and a triumph of the desire to understand despite all dangers.