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Captain Janek after receiving an invitation to Vickers' room, plays Love the One You're With on his little accordion.
Arguably, their whole exchange ("If you wanna get laid, just come out and say it") is pretty funny.
Ravel telling Janek "frankly, you're a shit pilot", as his reason to along with Chance, stay behind and help him crash the Prometheus into the the Engineer's ship, sacrificing all three of their lives in order to save earth. Also is a Heartwarming Moment.
"Vickers...are you a robot?" Not just the question, but the way he's smiling and pointing at her when he says it.
Never actually answered. I could still believe it.
Albeit one who must be fully functional and anatomically correct, presumably.
Fifield making a bong in his helmet.
Fifield's declaration once they find all of the dead bodies.
Charlie mentioning he never had to speak after a ghost, when the Weyland hologram finishes, before presenting his and Shaw's findings.
Depending on your view of it, David being a disembodied head for the last quarter of the film. Probably more so when he gets zippered up into a bag.
Before Fifield's and Milburn's descent into movie-genre-blind insanity, the exchange the two have with Captain Janek when they come across a pile of dead bodies and get told there's a life sign reading about one mile to the west of them...
One mile to the west, you say?
You know what direction that means we're going...
Hell Yeah. EAST.
David's "Didn't know you had it in you." remark. It is really, really Black Comedy.
Which he then lampshades and apologizes for, making it funnier somehow.
David's basketcycling and the shot with him carefully peroxiding his hair while watching Lawrence of Arabia.
Vickers angrily face-smooshing David. Even funnier after you learn they're essentially brother and sister.
Fifield, Milburn, and the alien cobra. What?! The scene was pure slapstick!