The Theft of the Enterprise is a very well done sequence. Hell, the whole MOVIE is pretty well done. I'm with Linkara, I think Kruge is actually a pretty well done character. Not to mention, really powerhouse emotion.
Kirk: "Now, Scotty."
Kirk: "The doors, Mr. Scott."
Scotty: "Aye, sir, I'm workin' on it."
Kirk: <oh S#!t face >
Good times, indeed.
Kirk's standoff against Kruge is also very well played; his stumble on learning of his son's death illustrated him at his most vulnerable (first Spock, now David).
Oh, yes. That scene was just so powerful and spoke volumes about Kirk's grief.
I think the whole Khan trilogy was awesome.