For me, the best part is that shot of Shaw looking up at the juggernaut looming above her, before it starts rolling. Actually that entire juggernaut crash scene, even the straight-line running. It's just so damned epic.
Scale is impressive, EPIC. I love the whole scene, the departure of the ship, race of Vickers in Prometheus, the ejection of cabins, collision, music, debris ... The achievement is amazing.
But there are so many good moments in Prometheus, the first 15 minutes are fantastic. The storm, C-Section (counting the discussion between David and Shaw, perfect), Orrery Scene. The discovery of the giant head, the vehicle enters the gigantic pyramid.
And the very end is great, mysterious and exciting. And finally we have a sequel....