Beam Me Up, Scotty!: It's often claimed that there isn't a single weapon fired in the movie. This isn't really correct, as there are two actual weapons firings (Kirk using his phaser to weld a door shut, and the whalers trying to harpoon George and Gracie) and one attempted (Chekov trying to stun the interrogation officers). This is likely a mix-up with a real fact, namely that this is the only Star Trek film with a body count of zero (assuming everyone survived the Probe's "attack", though Word of God is they did).
Big Dumb Object: The "whale probe". Presumably to to make a point about it being as thoughtlessly destructive to humanity as humanity supposedly is to whales.
Black Boss Lady: Audiences applauded when Madge Sinclair appeared as the (unnamed) Captain of the Saratoga at the beginning of the film.
Kirk: If we play our cards right, we may be able to find out when those whales are being released. Spock: How will playing cards help?
Dr. Taylor: Are you sure you won't change your mind? Spock: Is there something wrong with the one I have?
Book Ends: Kirk refers to the others as 'My friends' when they commit themselves to help Spock in Star Trek III ("My friends, Dr McCoy and I have to do this, the rest of you don't") and again after the resulting trial in Star Trek IV ("My friends, We've come home.")
Brake Angrily: Gillian slams the brakes on her truck after Spock declares that Gracie is pregnant.
Broken Aesop: Humans Are the Real Monsters. As noted in SF Debris' review of the film, why human actions that endanger the environment are brought up, the whale probe exemplifies the same traits, callous destruction of the environment and everything around for what appears to be just leisure, and yet while these traits are meant to be wrong for humanity, it's apparently completely okay for this thing because it's "intelligent" and not hostile, ignoring that anything that intelligent should know that it's causing damage, and that most environmental damage humans cause isn't done with hostile intentions towards what suffers from it either.
Actually, the Probe seems to be the only super-advanced robotic indestructible doomsday device in the Trek universe that isn't capable of judgement calls. Also, its designers (as detailed in the sequel novel) had a more 'Starfish Aliens' mentality than most of the species known to the Federation: the distinction between termite mounds and human cities might not be something they programmed into their machine.
It could be argued that, taking into account the unlikely nature of the threat and the overall Green Aesop nature of the movie, a better Aesop to take from the movie than Humans Are Bastards is simply that you should make sure you take care with what you have in the present in case you may need it for the future, including the environment.
Came Back Wrong: It's implied that maybe we didn't quite get all of Spock back at the end of the previous movie, that there's a certain... something missing. He gets better by the end though. Death apparently isn't something you can just get over straight away.
Cat Folk: The Caitian admiral at Star Fleet headquarters.
The Klingon Bird-of-Prey, which was just the enemy ship and later a means of escaping from the exploding Genesis Planet in the previous film, ends up being a vital part of this film's storyline thanks to its ability to cloak and land.
Kirk's glasses are an unusual case of this; from the perspective of the audience and Kirk himself, this is the last time the glasses are seen. However, 298 years down the line, they're going to be very important once again.
City of Weirdos: Most people are willing to accept the slightly out-of-touch Spock as a harmless stoner, even as he does weird things like jump into the whale tank...until he says things about the whales that he shouldn't be able to know. Truth in Television as anyone who lives in San Francisco could tell you.
Crazy Enough to Work: Even though it's the crew of the mighty Enterprise we're talking about, the whole "get some whales from back in time" thing did sound pretty ridiculous. McCoy lampshades this, to which Kirk simply responds that if McCoy has a better plan, he should speak up.
The film is also nice enough to explain why several saner sounding plans wouldn't work.
Critical Research Failure: In-Universe. The crew, knowing only the broad strokes of the sociopolitical environment of the late twentieth century United States, failed to realize that putting Chekov, a Russian, on the ground looking for "nuclear wessels" was a bad idea.
The first person Chekov asks is a Police officer, who just sits there with a blank look on his face.
Damage Control: Kirk asks when they can get their captured Bird-of-Prey under way, Scotty quips, "Damage control is easy; reading Klingon, that's hard."
Death Amnesia: Played with. Spock never says he can't remember what dying and coming back was like, but it was such an alien experience that he can't discuss it in terms anyone else will understand.
Actually, he states that he can't explain it without the other person having a common frame of reference, meaning:
Bones: You mean I have to die to discuss your insights on death?!
Dedication: To the crew of the Challenger at the beginning of the film.
Every Helicopter Is A Huey: Sulu tells a helicopter pilot that he trained on Hueys at the Academy, as a hobby (though the pilot probably didn't know he meant Starfleet Academy). The Novelization expands on it.
Face Palm: Kirk's reaction to Spock diving into the whale tank without warning him.
Foreshadowing: the Kilngon ambassador mentions attempts to negotiate a peace treaty, and that there would be no peace whilst Kirk lived. This may or may not have been intentional, but it's picked up as the central theme of the plot in the sixth movie—where, interestingly enough, the same character (and actor) is one of the first to applaud Kirk and the Enterprise crew when they prevent the sabotage of the eventual Federation/Klingon treaty.
Fish out of Temporal Water: The whole premise of the film, figuratively and almost literally, thanks to the cetaceans out of temporal water.
Gaia's Lament: Whales are extinct in the 23rd century. The probe is very unhappy about this.
The probe doesn't seem to have emotions, it just tries to communicate until something responds... if nothing responds, it never stops trying. (It just so happens that its communication drains Starfleet power supplies and screws up's Earth's surface weather...) The designers of the probe were callous and uncaring what side-effects this would have, just as the 20th century humans were callous and uncaring regarding the plight of the whales— at least that's the idea.
Possibly narrowly averted: the region St. Petersburg is located in is still named Leningrad Oblast.
Green Aesop: "To hunt a species to extinction is not logical."
Large Ham: John Schuck as the Klingon Hambassador makes Shatner look positively subdued.
"Behold, the quintessential devil himself: James T. Kirk, renegade and terrorist!"
Kicked Upstairs: Inverted: Kirk has violated orders to save the world. They "punish" him by taking away his cushy desk job and demoting him to a "mere" starship captain. So Star Fleet gets what it wants (a public punishment to demonstrate they don't tolerate such behavior, not to mention their best captain back in the field) and Kirk gets what he wants (the Enterprise).
Mister Sandman Sequence: An interesting version, seeing as it was applied to what was then the real-life present day.
Modern Humans are Morons: Kirk reminds his crew before exploring 20th Century San Francisco that "this is an extremely primitive and paranoid culture" and believes that no one pays attention to you in the contemporary age "unless you swear every other word." Bones is shocked to find a woman in a hospital on dialysis, asking if this is The Dark Ages, and compares two doctors chatting about a procedure to "the goddamn Spanish Inquisition." When he confronts the surgeon about to operate on Chekov, he manages to make it sound like an attempt to let the evil spirits out, and tells him to put his butcher knives away.
Averted strongly by Gillian, who manages to impress Spock and outwit Kirk.
No Antagonist: Even the probe is just trying to find out what happened to their friends on Earth.
No Endor Holocaust: We never do find out what happened to the crew of the Saratoga, or the other ships that the probe disabled en route to Earth. Who knows how many, if any, survivors there were on the ships where the life support was barely functioning, and the crew had to watch their emergency power run lower... and lower. Word of God, however, Jossed the idea that they died, and the novelization mentions in passing that the captain of the Saratoga managed to save her crew.
No One Gets Left Behind: When Chekov is at the mercy of 20th Century medicine, Bones insists on going to save him. Spock backs him up. When asked if it's the logical thing to do, he admits that it is not. It is, however, the human thing to do.
Oh Crap: The whaler's crew upon seeing the Bird-of-Prey decloak. Not only could the entire whaler fit in the Bird-of-Prey's torpedo launcher, but these are late 20th century humans. They have never seen an alien (or even human) starship of any kind before.
Once More with Clarity: During the time travel sequence, the lines spoken by the crew during the sequence are spoken later on.
The Other Darrin: The USS Enterprise that Chekhov and Uhura sneak into is actually USS Ranger, a then-standard oil-fired carrier.
Kirk advises Spock to blend in by "swearing every other word". While he has difficulty at first he finally grasps it, and, in perhaps a running gag, Spock has at least one in parts 5 and 6 as well.
The Quincy Punk: Kirk and Spock encounter such a punk on a bus in 1980s San Francisco. When he refuses to turn down the loud punk rock music he is playing, Spock nerve pinches him into silence, and everyone else on the bus applauds.
Rapid-Fire Typing: Scotty goes from not even understanding the concept of a computer without voice commands to apparently being able type 3 million words per minute. Also combines with Hollywood Hacking — the action on the computer's screen doesn't even remotely synch with his keystrokes.
Reality Subtext: At the end of the movie, when the crew are speculating what ship they're going to get:
Sulu: I'm counting on Excelsior.
Scotty:Excelsior? Why in God's name would you want that bucket of bolts?
This is a twofer: Harve Bennett, producer and writer of the film, had initially wanted the crew to end up commanding the USS Excelsior (which had been seen in the previous film) but was overruled; and Sulu himself ends up as captain of the Excelsiortwo films later.
Refuge in Audacity: Chekhov, in obviously Russian accent, going around the streets asking about "nuclear wessels" and getting away with it. Doesn't help him when he actually gets found on board one, however.
Rogue Human: The Klingon Ambassador tries painting Captain Kirk as this, in an attempt to get him extradited.
Sarcastic Confession: Kirk flat out tells Gillian exactly who he is and where he comes from over dinner. Subverted in that Kirk tells her with utter conviction and she naturally thinks he's full of shit.
Scotty and transparent aluminum. In the novelization, the engineer he sells the formula to is the one who introduce[d/s] it to the world, and Scotty discusses the trope specifically when McCoy calls him on it.
Scotty: "How do we know he didn't invent the thing?"
When Kirk sells his glasses at a pawn shop.
Spock: Admiral, weren't those a gift from Dr. McCoy?
Kirk: And they will be again. That's the beauty of it.
No one checks to see if removing Gillian from the timeline will change anything historic. Despite her insistence that "I have nobody here", no one considers the possibility that any future actions of hers could be important.
In the Expanded Universe, it's explained that this is actually standard Federation policy towards people from the past that wind up in the "present". If their removal from the timeline doesn't cause catastrophic changes, they're supposed to stay rather than risk polluting the timeline by going back with knowledge of the future.
Technology Marches On: Gillian mistakes Kirk's communicator for a pocket pager. Also the humour provided by Scotty using the then-cutting-edge Macintosh Plus as if it were hopelessly primitive is ironic nowadays.
Throw It In: They actually had Nichols and Koenig asking real San Franciscans where the nuclear submarine in Alameda was. The police officers staring suspiciously at the pair was a real cop who didn't know what was going on. The woman who answers, "Ooh, I don't know. I think they're in Alameda", had to be chased down to sign a release form for providing such a hysterical line in response to their queries.
Though it's very low-key (especially for Kirk) and doesn't really become much more than some flirting and a hug. Which makes sense considering the character becoming a female scientist was actually a fairly late revision to the script... in prior drafts, the character was a conspiracy theorist played by Eddie Murphy.
Totally Radical: Kirk doesn't quite have a grasp on 1986 idioms. Nor does Spock.
Kirk: And a double dumbass on you!
Trouble from the Past: The humans of the past hunted whales to extinction and that turned out to be a bad idea.
Unintentional Period Piece: Downplayed to an extent as it doesn't whack you over the head with The Eighties, but it has its moments. Gillian thinks Kirk's communicator is a "pocket pager", cutting edge in those days any time later she'd assume it was a mobile phone. The whole debacle with Chekhov being caught on board a US Navy ship is pure Cold War, and Scotty attempting to work a Macintosh Plus very much dates it. "Just use the keyboard" sounds like Dr. Nichols simply assumes that Scotty isn't used to computers with a mouse- cutting edge back then!
Unishment: When Kirk is demoted back to the Captaincy of a starship... which is what he wanted all along anyway.
Weld The Lock: Kirk uses a phaser to melt the lock on a door he locked some 20th-century medstaff in. This, incidentally, is the only time a phaser is fired throughout the entire movie (successfully—Chekov's attempt fizzles due to a malfunction), showing just how Lighter and SofterIV is compared to pretty much all the other films.
We Will Have Perfect Health in the Future: Demonstrated when McCoy, visiting a twentieth century hospital, is horrified that a woman is undergoing kidney dialysis. "Dialysis? What is this, the Dark Ages?" He gives her a pill, and minutes later, doctors are dumbfounded by her miraculous recovery as she grows a new kidney.