Many creators of Japanese media either lived through the Second World War, or have parents or grandparents who lived during the war. The atomic bombings of Hiroshima and Nagasaki left deep wounds on the Japanese psyche when it comes to the discussion of atomic weapons.
Therefore, any time a series needs a powerful Forgotten Superweapon, instead of an actual nuclear weapon (even if those are available), a bit of Applied Phlebotinum will be introduced that has the destructive effect of a nuclear weapon, but a different name. Great pains will frequently be taken to stress that these aren't actual nuclear weapons, even if they can level whole cities and/or destroy the world.
Any series that does decide to use nuclear weapons will usually portray them as A Bad Thing that must be destroyed at all costs, and only used by the most evil of villains. This taboo is even stronger in Japanese works, where the Three Non-Nuclear Principles are generally portrayed as being upheld long into the future in all but the most pessimistic of stories.
So far, this is Truth in Television. No nuclear weapons have been used in armed conflict since the Hiroshima and Nagasaki bombings. Two small direct wars (USSR vs China during the Sino-Soviet split and India vs Pakistan during the Kargil War) and several more proxy wars have been fought between nuclear powers without nuclear deployments taking place, though both NATO and Soviet combat doctrine for a hypothetical land war in Europe would have involved the deployment of battlefield [i.e. tactical] nuclear weapons.
Contrast our modern attitude about nuclear weapons to fiction of the pre-war eras in which devastating super-weapons were romanticized to the point of being able to end all war forever. For example, Alfred Nobel believed that if such a tremendously powerful weapon could be devised, the potential war casualties would become so high when compared to any possible gains that nations of the world would abandon warfare altogether. Following this, there would be no need for the weapons themselves, and everyone would just hold hands and get along. When real-life superweapons appeared at the end of World War II, military and political leaders still considered nuclear weapons to be really big bombs, but not inherently different than any other munition. The Nuclear Weapons Taboo only came as people learned about the hideous and lingering effects of these weapons and came to realize that nuclear war could push humans to extinction. Unfortunately, instead of ending warfare, it simply pushed human conflict into the realm of irregular proxy wars where non-superpower forces duke it out conventionally while the nuclear superpowers indirectly back their chosen allies.
If there is a weapon treated in a similar manner to nuclear ones but isn't referred to as such not because of censorship, but because it doesn't make sense in that setting, it's a Fantastic Nuke. Almost any series involving a Wave Motion Gun involves this. Compare Never Say "Die".
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Anime and Manga
N2 (Non-Nuclear) mines in Neon Genesis Evangelion. They're the largest and most destructive incendiaries ever invented, and they even create a mushroom cloud, but nope, they ain't nukes, hell no. They can somehow do this with a much smaller range than an actual nuke.
Truth in Television: Conventional thermobaric weapons like the MOAB have the thermal and overpressure effects of a tactical nuke, except that they are three orders of magnitude weaker.
Any explosion of significant power within an atmosphere will create a mushroom cloud (This can be seen on some of the bigger explosions on MythBusters). The cloud is formed by high-temperature gases and vapors produced at the site of the explosion rapidly rising as the "stalk" until they reach an altitude of equal density, whereupon it spreads out in the "cap". The idea that this effect is exclusive to nukes is a long-standing myth; the only difference between a nuclear and conventional mushroom cloud is the amount of radioactive material it contains.
The firestorm that destroyed Hamburg in 1943 was observed, by RAF planes, to take the form of a very large mushroom cloud. This was repeated in USAF bombing of Tokyo, with conventional weapons, in 1944-45. The physics involved was exactly the same.
It's outright stated that a number of cities, including "Old Tokyo", were nuked during the Post-Impact Wars that had raged in the early 21st Century. It even led to the presumed revocation of Article 9 of the Japanese Constitution (renouncing war "forever" and banning the government's right to declare an offensive war), and the establishment of the "JSSDF" (Japanese Strategic Self-Defence Forces). Considering the fact that they have 40-meter technorganic mechas developed from Angels, the idea that they were able to develop bombs with power roughly equal to smaller strategic nukes is one of their Acceptable Breaks from Reality.
The "Non-Nukes" still produce an EMP effect, however, as can be seen in the first episode of the TV series.
Some of the notes for the series label it a "positron explosive", which is a sort of antimatter bomb. An antimatter bomb would indeed have the yield of a nuclear weapon while not actually being a fission or fusion-based bomb, therefore not technically nuclear.
Vegatron bombs from UFO Robo Grendizer (one of the Mazinger Z sequels): It is explicitly stated they are radioactive, they are able to easily obliterate whole cities, the explosion forms a mushroom cloud, and they leave the land polluted with radioactivity. But no, they are not nukes. They are vegatron bombs.
"Reaction weaponry" in Super Dimension Fortress Macross needed official permission from the highest commanding officer within a colony before they could be launched.
Word of God has it that Reaction weapons were intended to be nuclear, at least in the earlier series, but that explicitly showing the good guys using nukes was a no-no at the time. So they've made it antimatter warheads (see above) instead.
It's notable that while Reaction weaponry is tremendously powerful, and capable of rending apart Zentradi warships, that this is NOT particularly powerful by Zentradi standards: in the second episode they manage to initiate a long range bombardment of a specific city on a specific planet with extreme accuracy from the distance of the lunar orbit with little problem, and later in the show a Zentradi fleet reduces an inhabited planet's surface to glass without actually using the forbidden Reaction weaponry.
In Macross Zero, Shin calls the Reaction Warheads the K? Monster monster fires nuclear.
Macross Ultimate Frontier displays the name of the target you're locked on in English (Britai's official Romanized name is apparentlyVrlitwhai). The "reaction missiles" from the last mission of the Dynamite 7 campaign are called "Nuclear Missiles" ingame.
In the Robotech translation, these weapons are rendered as "Reflex weaponry." It sounds like they're hitting the enemy with a giant rubber mallet right below its knee.
AKIRAleveled Tokyo as a trigger to World War III with "a new type of bomb," which turned out to be a psychic blast from the title character. Also subverted; in the manga, a nuclear weapon is used, and they make a big deal out of it.
In the Giant RoboOVAs, the shameful secret of Giant Robo wasn't that it was a massive engine of destruction commanded by the will of a twelve-year-old boy, but that it was powered by a nuclear reactor.
The backstory of Dai-Guard involves an "O.E. bomb" being used to destroy the original Heterodyne. There's plenty of angst in the series itself about when or whether the military should use one again.
The "Jignix" bomb in MD Geist: Death Force.
Zettai Karen Children appears to have a nuclear everything taboo, instead having "Neo-Clear" power plants. Which the Big Bad promptly steals nuclear Neo-Clear fuel from and sells it to the "Al Lugia Liberation Front" to make bombs. I wish I was making this up.
Despite all this it appears that lazy naming aside, Neo-Clear is actually something different as no fallout or even much damage results from one of the bombs. Though that may be to do with the Major containing the blast as he saw a local girl who bore a striking resemblance to Kaoru about to be caught in it. Needless to say, this annoyed him, resulting in the messy deaths of the terrorists.
Incidentally, based on the timeline, the start of the Time-Space Administration era, marked by the banning of mass-based physical weapons in favor of Magitek, takes place at around 1941, the year when Japan provoked America into joining World War 2. Coincidence?
In Heat Guy J most of the world's population has been destroyed after they appropriated the technology of the resident Superior Species. Originally, it was used for peaceful purposes (e.g. energy production), but people started wars using this Applied Phlebotinum. The survivors stopped trusting each other and closed themselves into seven city states, and the Celestials closely monitor any peaceful use of their technology. It's never stated what it is exactly, but it does sound an awful lot like nuclear power.
Axis Powers Hetalia manages to be about anthropomorphic countries, set partly during World War II, with the personifications of America and Japan as main characters, and still never mention nuclear weapons. Partly because the WWII part of the story never gets to that point (it's more or less abandoned by now), and partly because the series avoids showing the Darker and Edgier parts of history.
This is the same anime that managed to condense the entire Cold War into a condom joke that took less than two minutes. Yeah.
The A-bomb is central to the plot of Senkou No Night Raid but it's only ever called "new type of bomb." It makes sense: most characters don't know anything more about it, and those who know don't call it by name.
Hunter ◊ Hunter has the Miniature Rose, which instead of producing a mushroom cloud, produces a rose cloud. Furthermore, it also produces radiation (called Rose Poison). But of course, it's not a nuclear bomb, no. One of the few examples where such weapon is used for kind of good reason.
Warships in Legend of Galactic Heroes carry nuclear weapons, which makes it appear to avert this trope. However, the usage of nuclear weapons are limited to specific conditions in spacenote Beam weaponry are the mainstay in the series, and there is a taboo placed on using them on inhabited planets after a nuclear apocalypse in the backstory almost wiped out the human race.
In a major aversion of this trope for a Japanese-produced work, the first novel of Sentou Yousei Yukikaze reveals that Japan has nukes. On Faery, both the FAF & the JAM use nuclear missiles in their battles against each other.
In at least the early novels of Frank Herbert's Dune series, it is implied that most or all of the noble "Great Houses" have nuclear weapons (the "house atomics") but that the Great Convention which binds the houses together expressly forbids any house from using their atomics against another. Houses that do apply those weapons directly are usually cast out, losing their fief and becoming a renegade house. Of course, late in the first book, Paul Atreides indirectly uses the recovered Atreides family atomics against the Harkonnens and Corrinos when he blasts a hole through the stone Shield Wall near their landing site to allow sandworm riding Fremen fighters through to start a battle. He justifies this in that the prohibition only forbids using the nukes again human targets, and he only used it to level a portion of a mountain. In the second book, Paul himself, along with many of his soldiers and associates, was a victim of a nuclear weapons attack which left him blinded.
Adventure Hunters: War golems so horrified humanity that they were decomissioned soon after they were created. Centuries later, when the story takes place, most people don't believe weapons of such power ever existed and think of them as a myth. Those that know the truth encourage this mindset. The punishment for using them is life imprisoned in The Alcatraz.
The Return Of Godzilla is the big exception. The movie is about Cold War tensions, and even has a Russian nuclear bomb dropped on Tokyo in an attempt to kill Godzilla. Naturally, it goes very poorly, and actually revives the monster after a special Japanese aircraft had successfully knocked him down. Apparently, Japan was pretty fed up with having to tapdance between the two nuclear superpowers.
The Soviet director Leonid Gaidai exploited this trope as a way of Getting Crap Past the Radar to save his comedy The Diamond Arm from censorship. The film included controversial (by Soviet standards) scenes, such as a striptease, the protagonist's drunken debauche and an anti-Semitic remark by a rather unpleasant Soviet bureaucrat. Before showing the film to the censors Gaidai inserted the footage of a nuclear explosion into the epilogue. The censors, in a state of shock, allowed Gaidai to leave most of the film intact, on the condition that he cut out the nuke and the anti-Semitic remark. The Diamond Arm is now a cult film in Russia.
Live Action TV
There's a very odd Retcon example in the Doctor Who story "Genesis of the Daleks". In the previous Dalek stories, it had been repeatedly stated that the mutations that led to the Daleks were the result of a nuclear war on the planet Skaro. In the definitive origin story "Genesis", however, the word "nuclear" was never used and all the usual effects depicted in the story that one would associate with nuclear weapons (mutation, explosives that kill the slaves forced to handle them within a few days, massive destruction) were ascribed to mysterious "chemicals". It almost looks as if there was censorious Executive Meddling. The vast majority of fans, and subsequent canon writers, keep "Genesis" as the definitive origin but tacitly replace all references to "chemicals" with "nuclear" or "radioactivity" again.
It's never stated outright, but it's pretty damn obvious that the Killer Robots used nukes to wipe out most of humanity before Power Rangers RPM started proper. Ziggy mentions to Dillon how the ambient radiation interferes with both his compass and radio frequencies in their first meeting ("The Road to Corinth"), and later an orphanage consisting entirely of cancer patients is mentioned several times.
Inverted in Battlestar Galactica (2004). The entire show was based on dosing the audience with a September 11 reaction to watching nukes ruin every main character's day throughout the series. The pilot shows a whole planet being nuked from orbit. Justified, of course, since there's a war going on. While the Cylons have the majority of nukes throughout the series, the Colonials used a few themselves. One, to destroy a Resurrection Ship that kept humanoid Cylons from staying dead, and another inside an ancient baseship in the special episode, "Razor." Oh, and there was the matter of finding an Earth obliterated by nuclear war, and soon after, using several Colonial nuclear missiles aiding to destroy a Cylon stronghold in the final episode, "Exodus." You might as well have given the show a new title: Nuke 'Em: The Series. It appears that the Japanese themselves have not only enjoyed the American-based show, but also produced and watched comics and video games based on the series.
In Traveller nukes are restricted to the Imperial Navy.
While nuclear technology is known to be used by the Imperium of Man (the Death World of Krieg looks like the trenches of WWI due to a half-millenia of nuclear war), it sees little use in the game except for Rad weapons, and even then those are used for radioactive fallout rather than sheer destructive force.
In the Metal Gear franchise, the ability of the Metal Gear machines to launch nuclear weapons is basically the reason they are "bad." They also used a large railgun to fire warheads as sub-orbital artillery. Because these warheads were not technically part of missile systems, they did not violate several otherwise applicable treaties. "Loophole nukes" of a sort. Also, these weapons can't be detected the way normal nukes are, which completely destroys the concept of Mutually Assured Destruction; any country with a REX derivative can launch a nuke at another country and be guaranteed that there will be no retaliatory strike, because there's no way to determine where it came from or that it's even happening until the nuke hits.
Also, the Proto Metal Gears all had the advantage of being easier for Third World Countries to have Nuclear capability of their own. The greatest danger was that every Non-Superpower Country having such power would completely mess up global politics. Especially since they were willing to sell them to TERRORISTS or "Freedom Fighters" if the price was right. Imagine a world full of Osama Bin Ladens, and each having their own Walking Nuclear Death Mobiles.
Plus, the eponymous Peace Walker was essentially a nuclear platform programmed to launch even with false data, removing human decision making from launching and even preventing any practical counterattacks since its mobility allowed it to move quickly and avoid nukes, making it a truly terrifying weapon if attacked.
Metal Gear RAY was an exception, being the only Metal Gear with no nuclear launch capability. It was envisioned as an "Anti-Metal Gear" weapon that could counter the threat of other Metal Gears.
In Resident Evil 3: Nemesis, at the end, Raccoon City is destroyed in a huge flash of light that, to all appearances, would seem to be a nuclear explosion. However, in a later game, it's established that it was just hit by a whole bunch of conventional missiles at once. Note that in the real world, conventional explosions, no matter how large, do not give off the bright flash that is typical of nuclear detonations.
Inverted in Mass Effect 2, which features the M-920 Cain, a heavy weapon which produces archetypical mushroom clouds by firing high explosive slugs and nicknamed the "Nuke Launcher," despite not using any nuclear reactions.
Some language versions of World in Conflict call the tactical nuke that can be used in multiplayer a "BFB." Big Friggin Bomb? However, it's pretty obvious what it is a nuke, and the campaign plot doesn't attempt to hide it. However, they are only used as a last resort in the campaign, while it can be used with impunity in multiplayer given enough points. Not to mention that you get a medal for launching lots of nukes...
Advance Wars: Days of Ruin refers to Nemesis missiles (Climax in the European version) that were installed in both main countries by the IDS. They share a lot of similarity with the Cold War nukes the US and USSR were amassing, and might be in fact nukes, but the game leaves that open to interpretation, as they never launch.
Subverted in the first Shin Megami Tensei game. Not only are nukes referred to all the time, but partway through the game, a nuke gets dropped on Tokyo by the American ambassador who is really working for God, and the next parts of the game are 30 years later in the ruins.
The Japanese release of Fallout 3 had the entire questline related to detonating the nuclear weapon at Megaton removed. This also removes the Tenpenny Towers quests that open up in relation to it. The Fat Man launcher was renamed "Nuka Launcher" (Perhaps trying to connect more towards the fictional in game soft drink Nuka Cola), though this one should have been obvious considering that the name "Fat Man" comes from the bomb dropped on Nagasaki...
Ironically, the lightweight parts kit for the Fat Man in FalloutNewVegas still retains its original name of "Fat Man Little Boy kit" in the Japanese release of that game.
Used... differently in Singularity: There exist nuclear bombs, but the real focus is on an E-99 bomb that is a little bigger than a basketball and can turn the whole East Coast of your United States into a smoldering crater. Then there's the eponymous Singularity.
Command & Conquer 3: Tiberium Wars' German translation made aurora bombs out of the nuclear bombs because depicting weapons of mass destruction in computer games would lead to an X-rating of same game. There was a Kane edition which still had nuclear bombs (and suicide bombers) and was sold only to adults.
Command & Conquer: Red Alert 3 removed nuclear weapons from the game through a plot device while its predecessors used them amply. This no doubt had to do with the addition of a Japanese faction and someone rightly figuring that creating a game that you won by dropping a nuclear weapon on the Japanese might make someone mad.
The Soviet superweapon is still an ICBM-delivered WMD, however.
The original Ace Combat setting, Strangereal, is supposed to be an alternate universe of our Earth with approximately equal level of technological advancement. However, the only nation that apparently has ever developed its own nukes is Belka (essentially an alternate Nazi Germany) and even then their warheads counted in single units, not the thousands that world powers possess in Real Life today. For this reason, Strangereal's two superpowers Osea and Yuktobanian (counterparts of the US and Soviet Union) could duke it out in Ace Combat 5 in what would have basically become World War III in our world, without risking a nuclear apocalypse. In fact, when Belkan remnants try to use their remaining nuclear warheads in that war, the hostilities soon cease and everyone gangs up on the Belkans instead. That Ace Combat was developed by the Japanese company Bandai-Namco probably explains things. In fact, the reason the Ace Combat world erupts in large scale conflicts every few years is precisely because concepts like MAD and nuclear deterrence do not exist. Nations do not have the devastating power that nukes provide to counter-act aggression, and wars erupt as a result.
Belka is the only nation stated to have used nukes in a war. During the events of Ace Combat Zero, in an act of desperation, they resorted to dropping nukes on 7 of their own cities to try and delay the allied advance. The rest of the world was horrified at this, and may explain the world's preference for other types of weaponry. Backstory seems to suggest that nuclear weapons were not developed until the 1980s, instead of the 1930s and 1940s as in real life. Though nuclear power was apparently developed much earlier (nuclear submarines and reactors exist), which leads to a bit of a headscratcher as to why the technology was weaponized so late.
Even when Namco changed over to the real world in Ace Combat Assault Horizon, they played this trope straight. The Big Bad's super weapon, Trinity, was shown to have varying levels of destruction, ranging from vaporizing a medium-sized bridge, to destroying an entire city, and still having enough power to nearly knock the Protagonist off his feet from twenty or thirty miles away. However, Trinity has shown to have zero nuclear fallout, and by all means, it is still a conventional warhead, all things considered. In short, it's not a nuke, but a really, really big bomb (implied to be a MOAB-type weapon, only bigger).
The Reveal in BlazBlue: Continuum Shift that Kokonoe has been stockpiling nukes as a last resort against Terumi shows just how far Kokonoe is willing to go for the sake of revenge. Hakumen is horrified when he discovers this secret; claiming that the destructive potential of nuclear weapons surpasses even that of the Black Beast. He would know since he was present when nukes were used in a desperate bid to kill the Black Beast. The nukes completely destroyed Japan and, to add insult to injury, failed to stop the Black Beast.
Sid Meierís Alpha Centauri does not have nukes. Instead, they are replaced with Planet Busters, which have an even more devastating effect on the target and the environment (i.e. any city hit with one is completely wiped out, leaving behind a massive crater, unlike Civilization, where the effects are a little more tame). Using one is an unforgivable atrocity, however, and results in everybody declaring war vendetta on you.
In Rise of Nations, players can build nukes, but as soon as a player researches Nuclear Weapons, the Doomsday Counter appears on his screen. It starts at a number based on the number of players in the game, and every time a nuke is launched, it decreases by 1. Each time a player researches the "Missile Shield" supertech it increases by 2. If it ever hits 0, the game ends, with everyone losing.
The Empire superweapon in Perimeter is a SRBM note Short Range Ballistic Missile launcher with a tactical nuclear warhead, but it's simply called a "Ballistic Missile Launcher"
Starcraft: While nuclear missiles are used, they're very much Slap On The Wrist Nukes (even taking Units Not to Scale into effect), most buildings will survive getting hit by one. The reason for this is the backstory: An entire planet was reduced to glass and desert by an interstellar missile barrage of 1000 Apocalypse-class missiles. The aftermath was that such huge nukes were banned, but the smaller ones are permitted. Ironically, Arcturus Mengsk has absolutely no problems with nuking his own planet again if necessary (despite the bombardment being what caused him to rebel against the Confederacy in the first place).
NationStates has this pretty often in open RPs. The taboo seems so ingrained that even in RPs involving use of an unholy Lovecraftian monster and other WMDs, using a tactical nuke against said abomination is considered horrible.
Despite this, many nations maintain nuclear stockpiles for deterrence purposes.
The "Bleach Protocol" in Generator Rex, used as a last resort against particularly dangerous EVOs. Lampshaded in one episode:
Megas XLR has nukes in its arsenal, with warning labels around the Big Red Button. Coop wants to press it anyway, even when he and the enemy are in an underground military base at the time. Kiva insists that the nukes are not to be used, to Coop's disappointment.
One episode of Inspector Gadget has Dr. Claw attempt to launch an implicitly nuclear missile at Metro City, but nowhere is the "N" word used in the show.
Adventure Time dances very, very carefully around this, having a Mushroom War in its backstory and a distinctly After the End setting, while very carefully avoiding any reference to nuclear weapons as such - the word 'mushroom' is the closest we get.