[[caption-width-right:350:Emeril never cooked like this.]]

* Sulu's response to Ensign Rand after witnessing the explosion of Praxis and being warned off by the Klingons is hilarious in its snappiness:
-->'''Sulu:''' An ''incident''!\\
'''Rand:''' Do we report this sir?\\
'''Sulu:''' ''Are you kidding?''
* Bones after Kirk starts [[BoldlyComing sexing up a shapeshifter girl]] (though to be fair to Kirk, ''she'' kissed him):
-->'''[=McCoy=]:''' What ''is'' it with you, anyway?\\
'''Kirk:''' Still think we're finished?\\
'''[=McCoy=]:''' ''More than ever.''
** The next day, when they first believe they'd been had, then Marta as this disguised, very large creature corrects them before disappearing.
--->'''[=McCoy=]:''' What kind of creature is this? Last night you two were--\\
'''Kirk:''' ''[recoiling]'' ''Don't remind me!''
* Missed the best part:
-->'''Kirk:''' I can't believe I kissed you!\\
'''Shapeshifter!Kirk:''' Must have been your lifelong ambition!
** Can also work the other way around:
--->'''Shapeshifter!Kirk:''' I can't believe I kissed you!\\
'''Kirk:''' Must have been your lifelong ambition!
** As they're wrestling on the ground, they roll right over [=McCoy=], who tries to get out of the way but gives up.
* Another moment with the shapeshifter girl (named Martia) when she tells Kirk what happened when he kicked that one alien in the knee and made him collapse in agony:
--> '''Martia:''' Not everyone keeps their genitals in the same place, Captain.\\
'''Kirk:''' Anything ''you'' want to tell me?\\
''[Martia smiles]''
* All of Spock's machinations to delay their return to headquarters while they work out who shot the Klingon ship, when pressed by Valeris:
--> "A lie?" "[[DistinctionWithoutADifference An error.]]"
--> "A lie?" "[[MetaphoricallyTrue An exaggeration.]]"
--> "A lie?" "[[InsistentTerminology An ommission.]]"
** Made a hell of a lot less funny later on with [[spoiler: Valeris']] IronicEcho:
---> "A lie?" "[[TheMole A]] ''[[TheMole choice.]]''"
** If it had been Saavik, it would have been a CallBack to the funny moment in the second film when Saavik stares at Spock and exclaims, "You lied!", to which Spock replied, "I exaggerated."
* Kirk and [=McCoy=] have convinced one of the bad guys to finally explain what the hell's been going on... just in time for the ''Enterprise'' to find them and beam them up. Once Kirk realizes what's going on, he shouts "Son of a bitch!" and disappears on the last word, leaving it to echo for a while longer, and arrives in the transporter room cursing up a storm.
-->'''Chekhov:''' You want to go back?\\
'''[=McCoy=]:''' ''Absolutely'' not!\\
'''Kirk:''' It's cold...
* [=McCoy's=] reaction to General Chang's incessant [[LargeHam hamming]] is gold:
-->'''[=McCoy=]:''' I'd pay real money if he'd ''shut up.''
* "If I were Human, I believe my response would be... ''[FascinatingEyebrow]'' 'Go to Hell.' If I were Human."
* When Kirk tackles the Federation President at the end of the movie (to save his life, of course) he briefly introduces himself as "Kirk, Enterprise" while he's basically lying on top of the man. It's also the super-casual way he says it that makes it hilarious. One wonders if he meets his blind dates that way.
** Speaking of blind... the Federation President was supposed to be blind (the glasses he puts on to see the Operation Retrieval papers was a prototype of the [=VISOR=] Geordi wears on TNG), so after flying-tackling a blind man as weapons are being fired, Kirk thinks this is the way to help the man calm down!
* [=McCoy=] is on the witness stand in Klingon court and is asked his current medical status. He makes a joke about how it's fine, aside from a touch of arthritis. A SINGLE KLINGON laughs his head off while the rest of the assembled audience is quiet. Yes, some random Klingon in the peanut gallery thought that was the funniest thing he's heard all day.
** Doubled by Bones' smile right after. As far as he's concerned, he ''nailed'' that joke.
* The ship is scoured for the missing gravity boots and finally found among the belongings of Crewman Dax ([[Series/StarTrekDeepSpaceNine no relation]]). Chekov smugly deposits the boot in front of the crewman, with the declaration "If shoe fits, wear it." Problem is, the shoe DOESN'T fit, as the crewman can't wear standard issue boots because of the unusual shape of his feet.
** Capped by Uhura's FacePalm.
** Let's not forget Spock silently pointing to said crewman's feet when Chekov made his accusation. Spock's face usually doesn't change from a frown and it doesn't during this moment but somehow it looks more disappointed than usual.
** Also, one last time, Chekhov proudly claims something to be from Russia. Namely, the "Russian epic" ''Literature/{{Cinderella}}''.
* After the disastrous dinner with the Klingons, Kirk dictates his personal log back in his quarters.
--> '''Kirk:''' Note to the galley: [[GargleBlaster Romulan ale]] ''no longer to be served'' at diplomatic functions.
* Shortly after dinner with the Klingons and Romulan Ale, the ''Enterprise'' is picking up strange radiation anomalies:
-->'''Kirk:''' Mr. Chekov, you know anything about a radiation surge?\\
'''Chekov:''' ''[still suffering a wicked hangover]'' Only the size of my head.\\
'''Kirk:''' ''[groans]'' I know what you mean...\\
''[[[MoodWhiplash Torpedo careens towards Kronos One]] [[OhCrap and explodes, crippling the ship]]]''
* Rather a cruel joke, but in the last time Uhura ever appears in the credits of any ''Star Trek'' production (barring the 2009 movie), it's ''misspelled''.
* Spock convinces Scotty to waste time in order to delay the ''Enterprise'''s return to Spacedock.
-->'''Spock:''' Ah, Mr. Scott, I understand you're having trouble with the warp drive. How much time do you require for the repair?\\
'''Scotty:''' There's nothing wrong with the bloody thing!\\
'''Spock:''' ''[looming over Scotty to press the urgency]'' Mr. Scott, if we return to Spacedock as ordered, the assassins will surely find a way to dispose of their incriminating footwear and we will never see the captain or Dr. [=McCoy=] alive again.\\
'''Scotty:''' ...could take weeks, sir.
* After Chekhov wonders why the conspirators couldn't just "waporize" their uniforms and magnetic boots, Valeris demonstrates why by phasering a cooking pot out of existence, setting off an alarm. The OhCrap of the galley crew is funny enough as it is, but then Scotty ''and'' Uhura both come in through the end of the scene asking if someone fired off a phaser aboard the ship.
-->'''Uhura:''' Did somebody fire off a ''phaser''?!
-->'''Scotty:''' ''[angrily]'' Who fired a--?!
** In addition to those two, Chekhov has to hold back a pair of security officers rushing into the galley just a split-second behind Uhura, decked out in armor and phasers at the ready!
** Furthermore, the pot itself is vaporised but not its contents, which remains whole and standing perfectly where they are, complete with embedded whisk.
* A bit of Metahumor and StereotypeFlip during the briefing scene early in the movie. When Admiral Cartwright, one of the few black characters in the movie, predicts that the Klingons will become the "alien trash of the galaxy", watch SouthernGentleman Doctor [=McCoy=]'s "dafuq?" reaction. Given TheReveal about Cartwright's part in the plot, the humor wears off later in the film.
** ''Not'' so humorous to Brock Peters, however. He was rather uncomfortable playing a racist, having been on the wrong end of racist treatment throughout his life.
* The ''Enterprise'' officers coming back to the bridge for their RidingIntoTheSunset final scene:
-->'''Kirk:''' [[SoOnceAgainTheDayIsSaved Well, once again, we've saved civilization as we know it]].
-->'''[=McCoy=]:''' [[CallBack And the good news is]], [[Film/StarTrekIVTheVoyageHome they're not gonna prosecute]]!
-->'''Uhura:''' They might as well have prosecuted me. I felt like Lt. Valeris.
-->'''[=McCoy=]:''' Well, they don't prosecute people for having feelings.
-->'''Chekov:''' Just as well, or we'll all have to turn ourselves in.