* The whole "Stealing the ''Enterprise''" sequence, starting with breaking [=McCoy=] out of jail:
-->'''Kirk:''' How many fingers am I holding up? (''gives Vulcan salute'')
-->'''[=McCoy=]:''' That's not very damn funny.
** Then, when [=McCoy=] learns he's "[[SharingABody suffering from a Vulcan mind-meld]]":
--->'''[=McCoy=]:''' That green-blooded son of a bitch! It's his revenge for all those arguments he lost.
** Considering we now know George Takei is homosexual, this is HilariousInHindsight.
--->'''Sulu:''' ''Don't'' call me Tiny.
** Uhura's whole scene with "Mr. Adventure", from her epic stink-eye when he comments that her career is "winding down" to pulling her phaser on him and ordering him to get in the closet, while declaring, "This is fantasy!"
** Scotty explains that he's rigged the ''Enterprise'' for a skeleton crew:
--->'''Scott:''' A chimpanzee and two trainees could run her.
--->'''Kirk:''' [[DeadpanSnarker Thank you, Mr. Scott. I'll try not to take that personally]].
** The janitor in the Spacedock lounge, just staring as the ''Enterprise'' powers up and leaves its berth.
** "DANGER: SPACE DOORS ARE CLOSED."
--->'''Kirk:''' And... now, Mr. Scott.
--->'''Kirk:''' The ''doors'', Mr. Scott!
--->'''Scott:''' Aye, sir, I'm workin' on it!
** All of it building up to the EpicFail of the shiny new ''Excelsior'' and its revolutionary drive, complete with sputtering engine noises.
---> GOOD MORNING CAPTAIN
*** The sound of the engine stalling really just makes the whole sequence. It's entirely RuleOfFunny, but the laughs justify it 100%
* Even earlier than that, Bones' multiple failed attempts to pull a Vulcan Nerve Pinch on a Starfleet officer. Knowing that it's both him and Spock sharing the same mind during the scene makes it all the more hilarious with [=McCoy=]'s over-the-top OhCrap face.
-->'''[[MauveShirt Maltz]]:''' "[[MyGreatestFailure I do not deserve to live]]."
-->'''Kirk:''' "Fine, I'll kill you later."
-->'''Maltz:''' "You said you would kill me."
* Scotty and the talking turbolift with the oddly non-Majel voice on the ''Excelsior'':
-->'''Turbolift''': Level, please.\\
'''Scott''': Transporter room.\\
'''Turbolift''': Thank you.\\
'''Scott''': Up your shaft.
** That voice? Nimoy.
** The EpicFail that is the ''Excelsior''.
* How about this exchange between Kirk and Kruge on the rapidly-disintegrating Genesis Planet:
-->'''Kirk:''' You ''fool!'' Look around you! The planet's destroying itself!
-->'''Kruge:''' Yes, exhilarating, isn't it?
* Scotty finally lets Kirk know his secret to being a miracle worker.
-->'''Kirk:''' Mister Scott, do you always multiply your repair estimates by a factor of four?
-->'''Scotty:''' Of course, sir! How else can I keep my reputation as a miracle worker?
* Kruge gets in one. After killing his previous gunner for destroying the ''Grissom'' (when he wanted prisoners), Kruge eyes his new gunner and says, slowly, with a DeathGlare, "Gunner! Target engine only," then adds a dark "'''''Understood?'''''" as if to say, "Don't fuck this up, or ELSE." The gunner can only answer, "Understood ''clearly'', my lord." If a Klingon ever shit his pants, this was the time.
** The crew of big, tough Klingons who are clearly terrified of Kruge's pet.
* As the Enterprise enters spacedock, the people in the cafeteria watch it through the window, stunned at the enormous damage it sustained from it's battles with Khan. One of them is Janice Rand, who just shakes her head as if to say "Kirk, what have you been doing now?"