I liked Kirk's line in the Kobyashi Maru sequence about firing one torpedo to conserve ammo. I can't remember the line exactly but it cracked me up.
Also when Kirk walked by the guys he got in the bar brawl with and very cooly said, "At ease boys." Very Kirk-like indeed.
There were so many others, but can't think of them right now.
"Death, delicious strawberry flavored death!"