Slayers offers another example with the Giga Slave. In order to keep it from being Lina's answer to every problem, a Godzilla Threshold aspect was introduced. Lina learns that the spell could cause the world to turn to chaos, and vows to never use it again; naturally, she's forced to do so at the end of Slayers Next.
It's not always used when there's a climax. The end of season 1, like the end of NEXT, is one big attempt to get her to perform the spell. She doesn't. Almost the entirety of Try, once the characters learn who the Big Bad is, is about finding a way NOT to use it. They succeed, but Lina always accepted that she may have to use the Giga Slave if their plan didn't work.
Sugata of Star Driver has access to an extremely powerful first phase ability, the King's Pillar. However, every previous bearer of Samehk's mark who used the ability never woke up again. The time comes when he has to protect Wako, and well, you can guess what happened. Luckily for Sugata, his libido was strong enough overcome that effect.
Madoka in Puella Magi Madoka Magica is essentially a Forbidden Chekhov's Gunman. Kyubey repeatedly states that she'd have incredible, godlike power if she made a contract, but the other girls—especially Homura—keep preventing her from going through with it. Eventually, it becomes clear that her transformation would probably cause The End of the World as We Know It, because she'd soon become the witch to end all witches. Homura knows this would happen; being a time-traveller, she's seen it firsthand. But Madoka eventually makes a contract in a way that prevents the cataclysmic downside.
In The Flash storyline "Terminal Velocity", Wally has various reasons to believe that pushing his superspeed too far is a Godzilla Threshold that will draw him into the Speed Force, never to return. He tries to avert a conflict which he knows will force him to do this, but to no avail. However, when he does finally enter the Speed Force, he manages to return (which no one has done before) thanks to The Power of Love.
In the Astérix comic series, Getafix does not allow Obelix to drink the magic potion, as he fell into the cauldron as a boy, and an extra helping could have bad effects on him. But in one story, Asterix and Cleopatra (both the comic book and the animated version), Getafix gives him just a drop of potion to give him extra strength in a difficult situation.
Fone Bone, Gran'ma Ben, and one of the Dreaming Masters were the only people who didn't want to do it, but near the end of Bone, the Crown of Horns seems to be the only way out, even though it's been said that if Thorn even touches it, all of existence would be in jeopardy, and the trip there would be dangerous anyway with all the dragons that guard the Crown of Horns and intend to kill anyone who's anywhere near it.
Fone Bone improves their chances by not actually touching it, just grabbing Thorn's hand and almost touching it via static shock.
About a third of the way into Fantastic Four when the Four are running tests on their capabilities, Johnny gets so hot he melts the walls of the test chamber. Reed stops the test with fire retardant foam, then explains to him that he'd gotten almost as hot as a supernova and that this was bad. During the fight with Dr. Doom at the climax, Reed tells Johnny to go supernova inside Sue's forcefield to try and melt Doom.
More to the point, Death Blossom had never actually been tested; Grig worried that it might cause an overload and blow up the ship.
It's worth noting that the Death Blossom is never mentioned in the novelization, and instead is a prolonged space dogfight sequence. One wonders if it was a last-minute addition to cut down on film time (and CGI costs).
In the Lost in Space film, ships have hyperspace engines, but it is not a good idea to jump without coordinates or a jump gate as the exit vector would be random. The crew does this anyway when the ship is sabotaged and crashing into the sun.
Agent J in Men In Black is told by Agent K to never, ever touch the red button inside their car. When the two need to get across the city in a hurry and the tunnel is jammed, he is at last told to push the button — transforming the car into a high-speed rocket that drives along the ceiling of the tunnel.
In the second movie Jay uses "Pressed the Red Button" as a type of code, indicating that it is reserved only for the biggest emergencies. They seem to prefer to not even use the neuralyzer if they don't have to, so going for a rocket car ride would likely be a last ditch number on their list of priorities.
In Orgazmo, Choda Boy swears off using his dangerous "Hamster Style" at a young age due to its unpredictability, but at the movie's (heh, heh) climax, he employs it with great results.
In The Avengers, the whole team (minus Tony) spends a lot of time trying to keep Bruce Banner calm. Then the alien invasion arrives.
Captain America: Dr. Banner! Now might be a good time to get angry.
The Fast and the Furious: The Dodge Charger in Dom's garage belonged to his father and nobody, not even Dom, dares drive it...until the last ten minutes of the film.
Early in the Australian lawn bowls comedy (uh huh) Crackerjack, Jack tries a "flipper" - in short, a cricket thing transposed to lawn bowls - with disastrous results. He's angrily told never to pull that crap again, but when he has to pull off an almost impossible shot in order to win the championship, he's explicitly instructed to do it.
In The Rundown, Beck refuses to use guns because "bad things happen" when he does. In the final showdown he realises he has no choice, and bad things do happen...to countless mooks.
In the novel Foundation And Empire, Devers is trying to escape Trantor, with the police in hot pursuit, since he just killed a Lieutenant. He enters hyperspace very close to the planet, which could kill him.
It is promptly indicated that doing a Blind Jump like Devers did isn't actually all that dangerous, assuming you have enough supplies — if you vaguely target empty space (Devers skimped on calculations, and the higher the gravitational pull, the more complicated the calculations), you have a very good chance of arriving in empty space. The problem is that it is only useful to desperately flee, since you then have to spend a lot of time figuring out where you are before you can travel anywhere. Doing a semi-blind jump to a system, on the other hand... thus rendering this a cross-story Gun within the novel, since the protagonists of the second half of Foundation and Empire have to do exactly that.
In The Colour of Magic, one of the eight spells (eight is an important number on the Disc) has lodged itself in Rincewind's mind. He doesn't know exactly what it does, but popular wizarding opinion is that it will destroy the Disc (especially if cast alone). As a semi-sentient entity, it tries to cast itself. Rincewind barely prevents himself from casting it several times through the course of the first two books (which is one story) The Colour of Magic and The Light Fantastic. When he does lose control, a significant event is already happening and the seven other spells have been cast. At this point, it's not a spell to destroy the world... but to create others.
In the back-story of Going Postal, an automatic letter-sorting device with extradimensional components (it accesses a dimension where pi is exactly equal to 3) goes out of control, filling the Ankh-Morpork Post Office with letters. Wizards called in to inspect the device warn that shutting it down is likely to destroy the universe. Fed up with the machine, a veteran mail-carrier starts smacking the device with a crowbar until it shuts down. When the mail-carrier started hitting the device, the wizards ran away. As the doer of the deed testified; unless they had some other universe to run to, they weren't really sure about the danger. The wizards insist that the universe really was destroyed, but was instantaneously replaced by a complete, identical universe. That exact thing has actually happened before in that series. Twice, depending on how you count.
An unusual example, in that this was a ending-the-universe danger, but never actually crossed the Godzilla Threshold before it was destroyed.
The Chronicles of Thomas Covenant (at least the second one), after spending the last two series trying to prevent Lord Foul from obtaining Covenant's white gold ring in the final confrontation Covenant just hands him the ring. It turns out to be a massive Batman Gambit, as Covenant had finally come to understand how the white gold worked, and was able to trick Foul into destroying himself with the power.
Thursday Next has a switch located behind a pane of glass to break in event of "unprecedented emergency" — with the explicit note that "personal destruction" is not an unprecedented emergency. Unusually for this trope, the glass is not broken by the end of the book - but it is broken in the next book.
Live Action TV
In Babylon 5, the "Bonehead Maneuver" as mentioned in the Season 3 premiere. You have two ways of going in and out of hyperspace. If your ship is powerful enough, you can open your own jump point, or, if your ship isn't that powerful, you have a Jump Gate open one for you. You never want to open a jump point inside a jump gate, because this causes one massive explosion of a Negative Space Wedgie. Aside from the loss of a very hard to replace jump gate (typically a star system will have one at most) and potentially stranding people in the system if they lack massive starships, this doesn't actually cause any huge universe-altering affects. Just a huge explosion that is difficult for most ships big enough to open a jump point to outrun (so not really a Godzilla Threshold). They end up using the trick in a tricked-out new spaceship that MIGHT be fast enough to get away after using this trick to kill an enemy they DEFINITELY weren't big enough to fight.
In The Hitchhiker's Guide to the Galaxy, it's generally a really bad idea to activate the Infinite Improbability Drive on the starship Heart of Gold without proper programming, as anything could happen as a result. However, when confronted with imminent destruction by a pair of nuclear missiles, Arthur Dent goes ahead and does it anyway, since almost anything else would be an improvement. Luckily, the only thing that happens this time is a redecorating of the ship's bridge, and the two nuclear missiles being replaced by a live sperm whale and a bowl of petunias. (Also occurs in the book, TV series and movie adaptations.)
If we knew why the bowl of petunias thought "Not again!" while falling, we would probably understand a lot more about the universe. Later in the series, we find out EXACTLY why; it's one form of someone whose every incarnation keeps getting killed by Dent.It Makes Sense in Context.
Averted in the case of the button which, when Arthur pushes it, brings up a message that says "please do not push this button again". He doesn't push it again.
Warhammer 40,000 gives us the Spear of Twilight, which will doom whoever removes it from stasis to death from a wasting curse. Prince Yriel saved his Craftworld from being eaten by Tyranids by using it.
This is a commonly used tactic in Fiasco playsets, as usually the goal of the game is to create as atrocious a mess for the characters as you possibly can, so Objects (and, to a lesser extent, Needs and Relationships) with built-in bad ideas pretty much guarantees they'll be the centre of the action. A good example is one Object in "White Hole" - "Stasis gun. (Do not fire the stasis gun.)"
In the Men In Black: Alien Attack ride at Universal Studios, a Big Red Button like the one mentioned in the above example appears in every ride car. Like in the film, you are told never to press it. However, by the end of the ride you face a giant alien that's immune to your weapons. Guess what you have to do?
A cheesy instruction video seen while in line on the ride explains exactly WHY you don't press the button; it's a nuke capable of frying the more Kaiju-esque aliens.
Press X to Die is a video-games-specific instance of this, in which the game will really be over if the player actually fire the forbidden gun. Usually, the gun is some kind of weapon of mass destruction.
In the first Shadow Hearts game, all characters have a Sanity stat during battle. If this reaches zero, the character goes berserk, attacks their allies, and will not gain experience if you win the battle. The strategy in many difficult battles involves keeping this stat up while various effects suck it away. How does one unleash the final, most powerful transformations of the main character? By leveling the transformations up to max and then going insane while fighting in them. Something of a Guide Dang It.
In the Ultima series, the Armageddon spell (which kills everything and destroys the entire world when cast) has always just been used as a Red Herring to give the player a Non-Standard Game Over, but by sealing oneself inside the separate universe made by a Barrier of Life spell with the Big Bad in Ultima IX: Ascension, the player is able to destroy just the universe he's in right now, along with his opponent and himself.
The first Halo trilogy had you trying to prevent the Halos from going off. Guess what the last level of Halo 3 has you doing? It was only one Halo, not the whole set, but the concept remains the same. Cortana even handwaves it. The reason for trying to prevent that is that the Halos are meant to kill all life in the galaxy. The one in the third game is outside the galaxy as noted in the first level on the Ark. One marine points out that the Milky Way is visible in the sky, meaning you're not in it.
In Breath of Fire: Dragon Quarter, Ryu must unleash D-Breath against Chetyre in the true final battle until the D-Counter hits 100% to trigger the final scene - an action that earns a Nonstandard Game Over everywhere else.
Destroy All Humans! 2 this trope is played for laughs in one of the final missions. In order to stop the superweapon going off, Crypto must cross the beams of a targeting system. The entire Ghostbusters conversation is used verbatim on why this would be a bad idea.
In South Park: The Stick of Truth, the hero swears an oath never to fart on a man's balls, and is discouraged from this multiple times throughout the story. However, the hero is forced to fart on Zombie Nazi Princess Kenny's balls in order to defeat them.
In Castlevania: Order of Ecclesia, using the Dominus Anger, Dominus Hatred, and Dominus Agony glyph union kills Shanoa instantly. Guess what you have to do to beat the final boss? Though, as a result of a Heroic Sacrifice, Shanoa survives. Turns out that the glyph consumes a soul, not necessarily the user's. It just so happens that Albus was forced to hang around after his defeat and was able to take Shanoa's place. This is in the Good End. The Bad End has Shanoa die after using the glyph.
Fate/stay night. Specifically, using Excalibur, the first Deus Sex Machina (maybe), Shirou's arm, taking on Caster/Kuzuki directly on their turf (not a dangerous technique but the strategy is essentially suicide) and projection in general. Maybe it would have been best to simply leave this with no details considering how prominent this is?
'Shiki, you've got about thirty seconds before Roa takes over your mind? What are you going to do now?' Answer: Stab himself in his own point of death on the assumption that if his will is stronger than Roa's, he'll live through it and Roa will die instead. Still, it's not like Ciel had any other ideas, and Arcueid provided backup by way of a single drop of her blood. (Thus sharing her will with his and allowing him to overpower Roa with relative ease.)
Magicka lets you do this with the Arcane element and other elements to alter the beam's qualities, resulting in a combined, powerful beam. But if beams of opposing elements cross, a huge explosion occurs that will likely kill anyone nearby. Players may exploit this when fighting goblin shamans and other enemies that use beam attacks, intentionally or accidentally.
In Final Fantasy VIII, Ultimecia's end goal is to compress time. Because she exists generations into their future, the heroes end up having to allow her to begin time compression so that they can get to her to prevent her from compressing time.
Happens again in Ghostbusters: The Video Game, except this time due to being in the ghost world - where the same rules of physics don't apply, such as the lack of gravity on the actual landmass - one can probably assume that you can cross the streams without frying your ass to bits because the chances are reversed, thus making it more safe to try.
The Great Clock's purpose in Ratchet & Clank Future: A Crack In Time is specifically stated several times throughout the game to be maintaining time, not reversing it. Time-travelling with it would cause the entire universe to collapse on itself. Naturally, Clank has to use it to turn back time by only a couple of minutes at the end of the game after Azimuth kills Ratchet.
Metroid: Other M combines this with A Taste of Power for the Power Bombs. You test them out in the beginning of the game, and are promptly told to never use them, and in fact attempting do so will fail. Until the final boss, where you HAVE to use them after being swallowed. Also a Guide Dang It since you have, most likely, completely forgotten they exist by that point and wouldn't think to use them after all the hubbub about not using them previously.
RuneScape: Downplayed in the Rune Mysteries quest. You're warned not to play the lower registers on the giant organ because it'll make a loud noise and annoy everyone in the tower. Later, at the end of the quest, you need to bang on the keys to create a distraction.
The Lemmings series has the Nuke button, which can be used for a mass mercy killing if you screw up the level, or to sacrifice extra lemmings once you rescue the required amount.
The Evil Ring in the first Ys game normally kills you if you equip it. However, you later need to use it in combination with the Blue Necklace to access the area where Lair is imprisoned.
Super Robot Wars UX: The Orphes' Lepton Vector Engine which is a portable "Particle Acceleration Reactor". Basically what it can do is bypass space and time but the problem is that it damages human organs through continuous use. Think of it kinda like a semi-time machine but the pilot's getting microwaved.
This is the same way 8-Bit Theater character Red Mage's Ice-9 spell (a reference to the novel Cat's Cradle) works: as the description puts it, it removes all heat from the universe it is used in, thus destroying all energy. He can only use it on other dimensions, like a bag of holding that he shoved an enemy in... which White Mage then smashed with a hammer.
Played for laughs in A Very Potter Musical in which Harry shouts: "don't cross the streams!" when the trio summon their Patronus.
And Milfoy Malloy Count Chocula Malfoy. But the dialogue the Ghostbusters use is used in AVPM as well, though to dicuss why Harry has to compete in the House Cup tournament rather than beam-crossing.
Johnny Test—Johnny teams up with some villains to save the Earth, and they're told right before they head out to not use their powers while holding hands, since it could multiply their powers by 500% or something. Naturally, when their plans are thwarted, they turn to this. It sounded like the villains refused to do this, and Johnny teamed up with his... dog.
In Over the Hedge, characters tell Hammy not to drink caffeine, it could be dangerous to him, as he's already hyperactive. Later, they tell him to drink caffeine to go into Caffeine Bullet Time mode.
In one episode of The Real Ghostbusters, the GBs were falling toward a body of water from high enough to kill them on impact. Egon's solution? Have them fire at the water and cross the streams; the resulting explosion kicks up a huge column of water which breaks their fall enough for them to land safely. Upon landing safely, one of them asks how Egon knew it would have that effect. Egon's response? He didn't; he just thought it might help. We are talking about a guy who engaged in this exchange in the film:
In Transformers Prime the Autobots have the Spark Extractor in their inventory, they won't use it unless they really need to hit the Decepticons hard. They use it when they are fighting them on Cybertron.
In the classic Looney Tunes short "Design For Leaving," Elmer's house gets rebuilt with all kinds of futuristic gadgets (which don't work right, naturally). Among them is "this wed one, wight here," to which Daffy the salesman responds, "No no no no! Not the wed one! Don't ever push the wed one!" It's to escape tidal waves. It elevates the house hundreds of feet up into the air. When Elmer pushes it at the end, Daffy comes by in a helicopter to let him know that "For a small price, I can install this little blue button to get you down."
The Manhattan Project. Scientists did experiments seeing how close they could get radioactive cores to going critical without actually making them go critical. They called this Tickling The Dragon's Tail, and considered it a necessary but insanely dangerous thing to do. One core did accidentally go critical (very briefly) on two separate occasions, resulting in the deaths of two researchers and less severe cases of radiation poisoning for several others. They dubbed this one the Demon Core. And of course, there are two cases where they very intentionally let the cores go critical, but that was the point.
When an instructor is teaching you to use a gun, whether or not it's for self-defense, the first thing they will teach you is to never point a gun at a human being, with the sole caveat "unless your life literally depends on it". This is of course to prevent I Just Shot Marvin in the Face. Sadly, not everyone listens.