A few more from me...
Khan's teleport to Kronos
His arrival was incredibly badass. The Terminator-style crouch (none of that beaming from sitting to standing which annoys the heck out of me), the booming thunder (1000x more awesome in the theatre than at home). And the realization that he rematerialized somewhere very
Out of his depth in engineering, getting the job done but clearly struggling, trying to take responsibility for anything and everything... it was a small role but a memorable one. And of course, his fourth-wall bending reaction to "go put on a red shirt" was awesome.
During the space jump and fight from the cargo bay to the Vengeance bridge, my brain kept going "OMG Kirk and Khan are a TEAM!" One of those AU twists (culminating with Kirk and Spock in the warp core) designed to screw with longtime fans' heads.
Kirk (via Scotty) shot first. Was it a huge mistake? Would Khan have eventually betrayed him as explosively as he avenged Kirk's betrayal?
Science Officer 0718
An android? Cyborg? Trekverse Universal Soldier? Whatever he is, he's damn cool.
Big Fucking Ships
(another extra nerdy one)
The massive 16-deck saucer core, enormous shuttlebay and engineering sections on the Enterprise, and the ridiculously huge hanger 07 on the Vengeance. Yes, the reboot ships are much bigger than the old ones, and no it definitely was not unintentional or ignorable.
Khan's theme is my favourite of the nuTrek soundtrack.