Kirk telling Bones to drop the metaphors literally five seconds after I had the same thought myself.
The clear "Oh, **** me" look on Chekov's face when Kirk told him to put on a red shirt. I thought The Rains of Castamere was about to start playing...
Kirk/Spock's moment as Kirk was dying. Quinto blew me away, and then blew me away even more with his "KHAAAAAN!!!"
Pike's death and Spock/Kirk's reaction to it
Spock Prime warning Spock about Khan right after my rather enjoying seeing Kirk and Spock work together.
Khan's "You should've let me sleep" before crushing Weller's skull
The whole Enterprise going topsy-turvy.