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"That was the secret of secrets," said the Queen Jadis. "It had long been known to the great kings of our race that there was a word which, if spoken with the proper ceremonies, would destroy all living things except the one who spoke it."
Slayers quite famously has four: the most iconic is the Black Magic spell "Dragon Slave", and the most famous is the scaled up super-version, the "Giga Slave" — which taps into the power of the Lord of Nightmares and thusly will obliterate the entire universe if the caster loses control of it, something that makes its creator seal it away so it can never be used again. Both of the aforementioned are also Unholy Nukes There's also the Fire Shamanism spell "Blast Bomb", which is even more destructive than Dragon Slave, and the Astral Shamanism spell "Ra Tilt", which is equivalent in power to Dragon Slave but only targets astral bodies.
Ra Tilt and Blast Bomb, on the other hand, never suffer from this effect. Blast Bomb is more or less novel-exclusive, only appearing in the anime once in a scene that contained no comical exaggerations, and is noted mostly for being so mana-expensive that nobody since Lei Magnus has had the bucket capacity to actually cast it. Ra Tilt is an astral spell with no physical effects, so it's less funny.
The "Vegatron bombs" from UFO Robo Grendizer (one of the Mazinger Z sequels). Each one of them could obliterate one whole city, and left the land polluted with radioactivity in the wake of the explosion.
Mahou Sensei Negima! has Nagi reference this concept during the war when he mentioned his own world (earth) developing 'a very powerful bomb' that would end all wars. He said there were spells that were even more powerful available to mages.
Three examples are the 'High Ancient' (Greek) incantations: Khilipl Astrape (Thousand Thunderbolts), Kosmike Katasrophe (End of the World) and Ourania Phlogosis (Burning Sky). Their power seems to depend on the mage casting it, though.
They don't leave behind radiation. Aside from that, there's no difference.
Scrapped Princess has the Ginnungagap, a "Long Ranged Strategic Class Spell", one of a whole class of nuke spells.
In Naruto, the Bijuu and Jinchuuriki, giant monstersmade out of chakra and humans with the things sealed within their bodies, are treated like nuclear weapons by the ninja villages that don't simply shun and fear them. The First Hokage, the guy that at one point had control of them all, even gave most of the bijuu away to other villages to prevent them from shifting the tide of war too heavily and help grant stability. Pain and his organization have been kidnapping all the Jinchuuriki, intending to extract their bijuu and use them to rapidly start and stop wars to convince the other nations of their power as part of their plan to Take Over the World. However, his real plan turns out to be to create a superweapon capable of wiping out entire countries instantly, available to any country who's will to pay, and likely to be used if one side doesn't have ninja. After being used once he thinks people will stop war altogether out of fear, until someone uses it again, repeating the cycle.
In Chapter 572, a Tailed Beast Bomb clash between Kurama and 5 other tailed beasts creates a fireball that is about 50 times the diameter of a normal Bijuu-Dama explosion. Suddenly that "wiping out an entire country" idea sounds plausible. Kurama one-ups it by having Hachibi join in and creating a Combined Tailed Beast Bomb many times their size in a vain attempt to stop the Juubi's revival in 609. The resulting explosion could be seen from all the battlefields in the war.
Following Pain's death, Tobi instead wants to use their chakra to fuel Mass Hypnosis.
A special material in the second movie has the capabilities of producing infinite free energy, and served as the foundation of an ancient civilization, that was gone since then. In the climax, the mines where this material is found begin to collapse, threatening to wipe out the entire continent in one giant explosion. Hmm.
In Chapter 613 the Ten-Tails completely revives and is very reminiscent of a familiar mobile nuke launcher. In fact the first thing it does is launch a couple of hyper-Tailed Beast Bombs and destroy a couple of cities. Its range is so impressive some attacks take a few minutes to hit. Unlike a normal Tailed Beast Bomb, the Ten-Tails' bombs explode in a conical, rather than spherical, shape and can be seen the next country over.
The Ten-Tails, in frustration and having gathered more chakra, prepares a Tailed Beast Bomb similar to the aforementioned bombs, but as large as itself. Its explosion engulfs an entire sea.
Pain himself has a jutsu that creates a small gravitation pull towards everything in area that qualifies, given that he destroy Konoha with it. The real Madara also has one in the form a jutsu that calls in a gigantic meteor that's so big he considered it impractical to use in life because he had no way of making sure that he himself wasn't killed by it.
Lyrical Nanoha: The Time-Space Administrative Bureau possesses a shipboard weapon, the Arc-En-Ciel, that is described as a "magical distortion cannon" and is far worse than a nuke. Fired at a planetary surface it will consume everything for hundreds of kilometers. Fitting a ship with an Arc-En-Ciel requires extensive background checks and briefing for all crew who have access to the bridge, and firing it requires both two seperate verbal commands and a key-based interlock. The Arc might even adhere to the Two-Man Rule; the ship's technical specialist down in the sensor room appears to be the one who powers and arms the weapon, but only someone on the bridge can fire it.
In the Bount arc of Bleach it is revealed that the Soul Society previously used Jokai Crests to produce Reishi. They stopped using them and sealed the rest away under giant concrete blocks after one exploded and destroyed a 1/10 of the Seiretei, but now the Big Bad has absorbed one and plans to release its energy and detonate the others in a chain reaction. It's clear what the inspiration was.
Ulquiorra's Lanza del Relámpago he missed and it landed far away and still the Chunky Updraft still reach Las Noches.
Not to mention Soi Fon's bankai, which is pretty much a nuclear missile. She makes an anchor of sorts with a metallic sash to stop herself from being blown away by the blast.
In Trigun, the Angel Arms and (manga only) photon-ion cannon are often seen by fans as analogous to nuclear weapons in their effects and their power. As an exception, references to actual atomic bombs are made in the final chapters of the manga. The special reload of this weapon in Doom the Roguelike is a nuclear blast.
Almost subverted in the manga, which makes clear that the god warriors do emit plenty of harmful radiation.
In Hayao Miyazaki's film Castle in the Sky, the floating island of Laputa has the power to launch some sort of energy weapon that results in an explosion of nuclear scale.
The titular aircraft of Simoun possess extremely destructive capabilities, which are triggered by executing "Ri Maajons" - elaborate patterns in the sky usually performed in complex flight formations. Some Ri Maajons have the power to destroy several thousands of enemy aircraft and tanks in one go. That the Simoun are intended for use in religious services and are thus piloted by priestesses is rather ironic.
The titular Otome of Mai-Otome are weapons that singlehandedly win wars and determine a country's military strength. In the one major conflict since their creation, an entire country was wiped out, the survivors and their children suffering from debilitating illnesses. The underlying technology, if used peacefully, would improve the lives of millions. In the OVA, the various nations get together for Strategic Otome Limitation Talks (S.O.L.T.). And they're all entirely non-nuclear, nanomachine-powered, magical-girl maids.
The Black Cores from Dai no Daibouken, which are basically magic-powered nukes. (created from a rare ore analogous to the plutonium / uranium, nonetheless) On the back-story, one of them was powerful enough to destroy an entire continent.
Fairy Tail has a magitekKill Sat called the Aetherion, which fires a burst of magical energy to create a nuclear-level explosion. This blast also grows in power over time, if the initial burst is contained, like a chain reaction.
There's also Fairy Law, a spell that can annihilate everything in a radius of miles that the caster considers an enemy. If it's in the middle of a battlefield where you need to be selective about your targets, it's simply an extremely precise Wave Motion Gun that destroys enemies without hurting allies. However, if the caster were in enemy territory surrounded by enemy units, then it would probably rival Aetherion in it's capability for taking huge numbers of lives in an instant.
Then there's Acnologia Roar apparently capable of wiping out an entire island and leaves no traces.
When Louise uses Void Magic for the first time in Zero no Tsukaima the result is a flash of blinding light and then everything belonging to the enemy (that's what we see at least) spontaneously catches fire.
Dragon Ball started presented Ki Attacks as this with the introduction of Piccolo Daimou, who when restored to his youth, reduced a large city to a wasteland that extended beyond visible site during his fight with Goku. After Raditz's introduction, they were taken to Earth-Shattering Kaboom levels.
In Fallout: Equestria and its derived works, "balefire bombs" were instrumental in causing the postapocalyptic world described in the stories. They are clear analogues to nuclear weapons.
Referenced in Under The Northern Lights, an otherwise unrelated Friendship Is Magic fanfic. Twilight Sparkle stops a bomb-throwing assassin who seems to be destroyed by his own bomb when Twilight traps him and the bomb within a forcefield. Media and gossip make this into a "balefire bomb" to the ire of Twilight because balefire bombs are just theoretical weapons, no assassin is stupid enough to use a nuke-equivalent to kill someone, and nopony could contain a balefire blast like that.
In the Czech film Císařův pekař - Pekařův císař the golem is an obvious allegory for nuclear power. (The villains attempt to use the golem to rule the world and get killed in the process, while the hero goes to use it for the good of all.)
The civil war that breaks out between the wizards in Sourcery (as well as the earlier Mage Wars) has clear allusions to a nuclear war, though we don't get to see the truly powerful spells close up. There are areas mentioned repeatedly throughout the series but never shown where fallout from spells like this in ancient wizard conflicts make them uninhabitable. Finally, modern wizards essentially see it as their job to learn how to do magic and then never to do it, or at least not any of the seriously reality-warping stuff, aware of the Mutually Assured Destruction that Mage Wars had always ultimately caused.
There's a reference to the Mage Wars in Going Postal which makes this more explicit:
Any ignorant fool can fail to turn someone else into a frog. You have to be clever to refrain from doing it when you knew how easy it was. There were places in the world commemorating those times when wizards hadn't been quite as clever as that, and on many of them the grass would never grow again.
In Monstrous Regiment, Sam Vimes makes explicit reference to the "first use of magic" in a war... a clear parallel with nuclear weapons.
Pratchett is quite fond of using the adjective "thaumaturgical" in relation to the Mage Wars, which does the double duty of being Disc science's equivalent of the word "atomic" and bearing a cosmetic similarity to "thermonuclear".
Reaper Man we get to finally see one up close. It was powerful enough to destroy an entire living city.
Pratchett was in fact formerly a scientific journalist specialising in nuclear physics, so his books are full of in-jokes about the subject.
The Science of Discworld involves the magical equivalent of a nuclear reactor, designed largely from information contained in scrolls found in a cave in a dangerously magical area (everyone who went there died of rare, magically induced diseases) in the form of a bowl-shaped valley surrounded by rings of mountains. When the thing begins to overload, Ponder Stibons says he thinks that the reactor at that site probably was shut down in this state, so they need to come up with a way to bleed off the magic FAST.
And inverted in Jingo, where it's implied that Leonard of Quirm has designed a bona-fide nuclear bomb (the materials it's made from "don't like being squeezed. So they go bang. With extreme alacrity.") This is one of the many reasons he's kept locked up.
The Last Hero gives us Agatean Thunder Clay. Cohen the Barbarian and his Silver Horde fill a fifty-pound keg with the stuff and plan to deliver it to the gods. Such an explosion would not only blow up Cori Celesti, but also erase the Discworld's magic field. and with no magic, there would be no Discworld.
Tolkien got tired of people viewing the One Ring as an allegory for nuclear weapons. He was fond of noting that if the Ring was an allegory for the Bomb, Saruman wouldn't have tried to steal but, instead would have tried to develop his own, and the Alliance would have used the Ring against Sauron.
Although, strictly speaking, Saruman DID create his own Ring, although it was never used as more than an indication of how mad he had become.
China Miéville's Perdido Street Station makes mention of Suroch, an area of the world that's been... twisted after New Crobuzon dropped a "torque-bomb" on it. Torque... twists things. That's what it means in physics, and that's definitely what one would call the results. The descriptions of Suroch try to avoid saying anything explicit. Apparently it was part nuke, part key to the gates of Hell. It can even be considered to be worse than Hell because demons are scared of the things that have crawled out of there.
"Colourbombs" in the same setting are implied to be less wrong but even more destructive; Mieville's influences being what they are, this latter might bear some relation to "The Colour out of Space". Colourbombs were used to cover up whatever the Torque did to Suroch. Basically, it was better to blanket nuke the area than try to explain the effects of torque to the populace of New Crobuzon.
The city-killer (aka Hecatomb) in Iron Council is beyond even colourbombs (another kind of fantastic nuke) for sheer alien annihilation. It ERASES CITIES. And casts ripples of destruction BACKWARDS IN TIME.
The Deplorable Word in The Chronicles of Narnia is a magic spell that destroys all life in the world save that of the person who speaks it. We see a world where it was used in The Magician's Nephew, complete with not-so-subtle allusions to nuclear weaponry.
The seventh book of The Sword of Truth series has a wizard activating an ancient spell in the middle of the enemy camp. The results are quite nuclear, and cost the enemy about a million soldiers.
The Legend of the Seeker TV series that is loosely based on the books features Whisperers, which are cylinder-shaped containers that hold the screams of the shadow people. When released manually or via the timer, the Whisperer emits an ear-piercing scream that kills very living thing within a league. Only creatures that can hear are affected, so a wizard may be able to place a temporary deafness spell to protect everyone in the affected area. Not surprisingly, used as weapons of terror by both the D'Harans and the more extremerebels.
Which is a mix of two different concepts from the books. The first is the shadow people, incorporeal wraiths killing anyone touched (used by Darken Rahl's father), which were actually fought with sonic weapons. The second is the Dominie Dirtch, stationary stone bells serving as a border defense of a country. These shredded anyone in front of them when struck from behind. Plugging one's ears as a countermeasure was implied to have been used a couple thousand years ago; it was recommended again during the books, but the weapons were destroyed before it was needed.
The Wheel of Time has Balefire, which obliterates the target in the past, leading to a whole load of complications when linked circles with sa'angreal started using it to blow up cities during the War of the Power.
The Choedan Kal, a pair of Amplifier Artifacts exponentially more powerful than any others in existence, also tend to invoke this trope. While one eventually melts during the Cleansing of the Source, Rand ultimately destroys the other precisely because the destruction even one alone can cause is so great.
It goes even deeper then that. When Rand grasps the full power of the Choedan Kal, he concludes that even the single one he has is more than powerful enough to bring all of reality to a crashing halt, forever.
Unravelling, or taking apart an existing Weave of Power, can cause massive explosions. For extra points, do it to a Gateway and survive.
In John Moore's Bad Prince Charlie, two neighboring kingdoms are both trying to find a "Weapon of Mass Magical Destruction" left behind by a previous king.
In the Age of Unreason series, France uses alchemical magitech, building on the theory of creating resonance between two objects to make them attract, originally used to make target-seeking cannonballs, to attract an asteroid to London, creating the equivalent of a nuclear winter. This "Newton's Cannon" gives name to one of the books in the series.
In the backstory of the series proper, a war was fought between rival Great Mages, aptly termed the Mage Wars. It culminated in the total and near-simultaneous destruction of both enemies, along with their respective strongholds, which were filled with magical artifacts. The resulting Cataclysm gouged vast craters and reshaped the entire continent, an event so powerful that it echoed through time to recur three thousand years later.
To a lesser extent, a sufficiently powerful mage can perform a form of Heroic Sacrifice called a Final Strike, expending all their magical power and any they can draw from their surroundings in a massive detonation. When Vanyel did this, he scoured a mountain pass down to bedrock and destroyed an entire invading army. In life, Vanyel was explicitly stated to be capable of leveling cities all by himself.
Xhum Y'Zir's Seven Cacophonic Deaths, in Lamentation by Ken Scholes.
The Andadt from The Long Price Quartet make nukes seem like pop-guns. The Andat "Sightless" blinds the entire world, right down to the insects.
In Lawrence Watt-Evans' The Legends of Ethshar novels, there is a simple spell that can permanently negate magic within a huge volume. This is a bad thing in a world that heavily depends on magic and is one of the reasons that no one makes flying castles anymore. Naturally, the wizards of the world have gone to great lengths to expunge knowledge of it from the world.
In the Silver Tide by Michael Tod, the real reason given for why Grey Squirrels so rapidly displaced Reds in Britain in the 1960's is that as they can count in binary they can use numerology to tap into "stone power", creating squares that give of waves of energy, making anyone inside nauseous with small squares (sixteen stones) or killing everything inside with larger squares (4096 stones), disrupting ley-lines with its power, and sending waves of nausea and evil across the landscape. When one of the Red’s learns to count (base eight, non-binary), they retaliate with numerology powered Beam Spam.
David Weber's Wind Rider series had a group of spells used to "strafe" the continent of Kontovar, killing everything not under the most powerful black wizards' shields.
George R. R. Martinhas also stated that he thinks of the dragons as a counterpart to the nuclear deterrent. This makes Daenerys the most powerful person in the world and Martin wishes to explore in his writing whether weaponry power can be used not only to destroy but also to accomplish something good.
Inverted in The Dresden Files, where involving vanilla mortals into a supernatural conflict is likened to using nukes; in part because humans have regular old nukes, in fact (the other reason are, in order, that the sheer force of numbers means that whoever gets the humans on their side basically wins, and pretty much the entirety of human folklore consists of a long how-to guide on dealing with the supernatural).
The closest thing TDF has to a straight example is the Darkhallow ritual, the most potent necromantic spell to date, which sucks the area dry of all living and undead energy for many miles around the caster. Although it should be noted that this is only a SIDE EFFECT of the spell, the purpose of which is actually to make the caster a god
Another, smaller, example is the Death Curse, which is the ultimate Taking You with Me attack, in which a Wizard uses all their magic and all the energy keeping them going in one go. The effects can vary based on power and, more importantly, based on intent - it can either be immediate and destructive, like turning a city block to glass (and probably more, in the case of the Senior Council), or, perhaps, more long term, like Harry's mother's, which crippled Lord Raith by preventing him from feeding.
Eragon Literally. Any sufficiently skilled magic-user can create a nuclear blast by uttering "Be Not" in the ancient language, converting their mass to energy. This is how the Rider Glaeron killed several Forsworn and turned Vroengard into Mordor so Galbatorix wouldn't find the hidden cache of Eldunari and dragon eggs. It's also how Galbatorix tries to pull a Taking You with Me after Eragon and the Varden have beaten him in the climax. Angela can seemingly also do it, but vows not to unless there is absolutely no other option to win a battle.
Harry Turtledove's Darkness Series has a magic nuke in form of the unnamed product of the Naantali Project, a Kuusaman mega-spell that utilizes a link between the laws of similarity and contagion. It makes use of animals (or, theoretically, people...) that are grandparents and grandchildren of each other, pushing the elder one forward in time and the younger one back in order to create a massively destructive discharge of sorcerous energy that can be directed anywhere on a map.
In The Malazan Book of the Fallen, this is the origin story of the Crippled God. A cabal of wizards decided that High King Kallor needed to die, and so used their magic to ensnare a god, which they then launched at Kallor's head. The God's impact destroyed an entire continent, devastated the God's very being, and failed to kill Kallor.
The Fiendfyre spell from Harry Potter borders on this, being an extremely destructive spell that can even destroy Horocruxes, but it is EXTREMELY hard to control and is as likely to kill the caster as it is the intended target.
In fairness, it might be unbelievably easy to control, all we know for sure is that Crabbe wasn't listening when when the Carrows told him how to stop it. The numpty.
In the Star Wars Expanded Universe, this is how turbo lasers on large starships are depicted when fired at planets, with cases of things like three Star Destroyers bombarding a planet for a day, and by the end of it it was completely uninhabitable.
In Roger Zelazny's The Chronicles of Amber anybody who passed though the Logrus—the maze-avatar of pure Chaos—and received sufficient training in magic is able to summon raw Chaos to permanently destroy everything in the designated area. The destruction can be localized, but there seeps to be no upper limit on the area size. The protagonist Merlin explicitly compares this to calling in a nuclear strike, since Chaos obliterates everything in the area, even evidence or things that are of interest, and there's no way to stop it. Only to escape. A variation of the spell surrounds the caster with a slowly advancing wall of Chaos. Merlin cast it twice: once by accident, once to threaten an enemy.
In earlier Zelazny's series Dilvish the Damned Dilvish escaped from hell with the knowledge of several highly destructive dark spells. Unfortunately they are way too powerful and devastate an area as large as a city. He refrains from using them most of the time for much the same reasons.
Live Action TV
Doctor Who: The war that led to the creation of the Daleks was not fought with nuclear missiles, but in fact "Neutronic missile". Presumably this was done because it gave them more creative freedom over what they could say the weapons do/did, for example real nuclear missiles would just burn or vaporise a jungle rather then petrifying it.
Warehouse 13: The brick from the House of Commons is said to have contain the entire force of the London Blitz. Artie calls it out as an "Artifact Nuclear Device".
The Minoan Trident in the season 2 finale. If struck into the ground three times it causes huge earthquakes. Do it near a supervolcano and you don't just get a nuclear-level blast, but the ash causes the equivalent of nuclear winter as well.
Mythology and Religion
Hindu Mythology and numerous associated stories described the Brahmastra, a weapon that could only be used by someone who had meditated on the god Brahma and possessed the highest levels of concentration that could completely obliterate its target in a single strike and would never miss, but would destroy all life in the area and render everyone nearby sterile. Yes, the ancient Indians were talking about nukes before nukes were invented.
If the fringe theorists are to be believed, it really was a nuke. Scientists measuring the level of radiation in Rajasthan found out that the area has been suffering from high radioactive levels since more than 10.000 years ago. Combine this with vivid description of (what is today understood as) nuclear warfare in certain Hindu scriptures, and you really wonder whether this is a Real Life case of And Man Grew Proud.
Exalted has the Soulbreaker Orb, a magical device that, when triggered, simply kills anything in a five-mile radius. No actual damage is done, there is no giant fireball, everything just falls down dead. Of course, this being Exalted, it probably means that your character will survive with a minor scratch.
Also, the Imperial Defense Grid and some of the Solar Circle spells, such as Rain Of Doom and Total Annihilation.
The Thousand-Forged Dragons also count, being weapons of mass destruction that can utterly destroy local geomancy. Since Ley Lines and demesnes are the source of...pretty much every natural phenomenon and quite a few non-natural ones, this makes nuclear fallout look like a fairly minor side-effect in comparison.
Exalted has a LOT of Fantastic Nukes. Other canonical ones include the Gunzota Device, which turns every living thing in a several-mile radius into amethyst statues, and the Godspear, a Wave Motion Gun that does infinite damage to anything in its line of fire.
Then there's the Eye of Judgment, a larger, less resource-efficient Godspear that kills everything within five miles or so of the target ground, mounted on a flying castle.
Some of the Malfeas Charms for the Infernals are obviously building up to this, at least in the hands of homebrew. The "Green Sun Nimbus Flare" charm tree allows you to turn opponents into mushroom clouds and inflict magical radiation sickness on hell steroids on your enemies. Who knows how this could end up by Essence 10? There's even a Malfeas shintai charm that basically turns a significant area around you into Ground Zero except to allies and people who grovel at your feet.
Magic: The Gathering has a fair number of mass-damage and mass-destruction cards, usually rare. World-killing spells are often much cheaper than one would expect. For example, calling down God to destroy the world costs the same amount of mana as summoning an antelope. The Golgothian Sylex is probably the most famous example: Urza used it to destroy Argoth, which led to nuclear winter and an ice age. However, the card only destroys Antiquities cards, which makes it nearly useless. Other classic examples are Armageddon (destroys all lands), Nevinyrral's Disk (destroys everything except lands...okay, and nowadays planeswalkers), and Wrath of God and its alternate-universe counterpart Damnation (destroy all creatures, no regeneration to weasel out of it). Obliterate destroys all artifacts, creatures and lands, which can't be regenerated — and unlike the others, this spell can't be countered. Possibly the most devastating example printed to date, though, is Apocalypse which simply removes everything currently in play from the game, thus killing it Deader Than Dead...
There are also Soul Bombs, which are powered by a sentient being's ethereal spirit, which were used by Urza and his strike team to destroy most of Phyrexia.
The first D&D nuke is from the World of Greyhawk, the Twin Cataclysms: the Invoked Destruction and the Rain of Colorless Fire, which sound a lot like a nuclear blast and fallout. This destroyed the the Bakluni and the Suloise nations and left a desert waste.
"Apocalypse from the Sky" spell is a legal, non-epic, destructive spell in 3rd Edition with a ten-mile per level radius centered on you (and due to fact that you have at least to be level 18 to cast the spell you can imagine the blast), and, unlike any other spell, you can't exclude yourself from it, and even if you do survive that, the corruption damage would probably put you in a coma.
In 3.5, a wizard can use a number of feats to make almost any spell dangerously explosive. Combine this with the spell "Locate City", which has a range of HUNDREDS OF MILES, and the results speak for themselves. The "locate city bomb" works like this: take Locate City (range: 10 miles/level), apply Snowcasting (making it [cold]), apply Flash Frost (adding 2 cold damage to everything in the area), apply Energy Substitution to make it electric, apply Born of the Three Thunders to change damage type and add a reflex save to avoid half the damage, then apply Explosive Spell, forcing a Reflex save vs being blasted to the edge of the area, taking 1d6 of damage per 10 feet traveled (so, at the center, it's 5280d6/level of falling damage). It's actually much trickier for a Wizard to pull this off than for a Sorcerer to do the same, owing to the interaction of feats which can't be applied until the spell is actually cast and a Wizard's need to prepare spells in advance.
A few noted problems: The spell is definitionally two-dimensional (a circle), meaning it might propel its targets only a few feet up or knock them to the ground to send them to its closest "edge". Also, any obstacles hit by anyone in the radius simply deal 1d6 damage and cause them to stop traveling.
The spell actually has a three-dimensional spell, as the description mentions being able to locate subterranean cities, provided they are easier to get to than their surface counterparts.
A variant (and less rules questionable) is to apply fell drain (negative level to anyone hurt) which turns anyone in the radius with 1 hit dice (most small animals, including vermin, count and, depending on the DM, most NPCs, qualify) into wights which promptly kills anything left and make more wights, instead of everything after Flash Frost.
Things like Meteor Storm might count, at least given Obsidian's interpretation of what they look like.
Mystara, according to The Principalities of Glantri (Dungeons & Dragons Gazetteer), has a force known as the Radiance meant to amplify magical powers. One of the spells related to the Radiance is a fireball variation that creates a mushroom cloud, and causes some form of sickness for those who remain in the area.
Forgotten Realms had a few. The most destructive single spell about which there's some lore and not just mentions is "Killing Storm" from Elven High Magic. During ancient elven wars, these blasted one kingdom so thoroughly that after 11,000 years the place remained a moor.
In the Eberron campaign setting, the entire nation of Cyre was destroyed during the Last War by an event known as the Mourning. A thick mist covered the country and killed anyone caught in it. While the particulars of the event itself seem rather un-nukelike, the devastated Mournlands are described in a way reminiscent of an area destroyed by nukes and heavily contaminated by fallout, including a "Glass Plateau" and a rift in the ground that glows with eerie light and mutates anything that stays too close too long.
The Skaven of Warhammer made a literal nuke out of Wyrdstone. It's currently armed but undetonated, sitting under the human city of Middenheim.
There's a spell as well that drops an asteroid on the battlefield. It can wipe out castles, and half the opposing army when timed right.
Curiously enough, Warhammer 40K doesn't have that many nuclear weapons (which is not to say they have nothing that does as much daage, oh God Emperor no). They feature in Krieg's backstory (a rebellion ended in a century of atomic fire, after which the population took atonement and trench warfare as their hat), and some Rad weapons (weapons that use radioactive fallout, not slang).
Cyclonic torpedoes are the most popular method for delivering an Exterminatus that burn away oceans, atmosphere, and anything alive (and an advanced version that kills the actual planet).
Orks have an extremely effective method of travelling through space and conquering planets: Find really big meteors and asteroids, hollow them out and make them airtight, and fit colossal engines and reactors for propulsion. When they arrive on a planet, they either survive the landing, causing thousands of orks to crawl out of the wreckage looking to finish off the survivors, or it explodes midair, resulting in a ginormous explosion, which is almost as much fun to them.
The tabletop RPG Hackmaster has a spell named Fireball: Nuclear Winter.
Its range is several hundred feet, while its area is several miles. Needless to say, casting it is a bad idea unless you're immune to fire.
Mage: The Ascension had a set of items called selective mines. Each of them looked like a large landmine and when properly activated, would totally devastate everything in a large radius - except for a small group of people selected by the user. Handy.
The Order of HermesSplat book included the rote "Ball of Abyssal Flame", basically a really powerful Fireball that also converts matter in the target area (essentially disintegrating it) into Quintessence to directly fuel the spell. Associated with the destructive House Tytalus mages.
Mage: The Ascension also included "spirit nukes" in the metaplot, although exactly what they were was a little inconsistent. Their story use was apparently to imply hubris on the part of the Technocracy, despite the fact that they were used on a nearly unkillable vampire; different sourcebooks said different things about what would've happened had they not been used. In any case, they ripped people's souls apart in addition to the physical damage, and wrecked the spirit world globally.
The 10th level Black Hole spell is fun if you've ever wanted to cause a three mile swath of obliteration and piss off the entire planet doing it.
The apocalypse in Deadlands: Hell On Earth came about with ghost rock bombs, nukes made with irradiated Green Rocks. The physical destruction from a "city buster" is fairly limited, but it then releases a storm of damned souls that kill everyone within a 100-mile radius.
Divine level spells of certain paths (and even certain Ki attacks) in Anima: Beyond Fantasy qualify as this. At the most extreme cases of the former, the spells affect everything within a radius of 1 AU (150,000,000 kilometers).
The old computer game Wizardry had the Tiltowait spell.
"The effect of this spell is somewhat like the detonation of a small tactical nuclear weapon."
From the same era, the original BardsTale games had a spell named Gotterdamurung. The four-letter codeword used to cast it? "NUKE."
Wizardry VI through 8 went one better with the Nuclear Blast spell. Description: "A miniature fusion bomb".
Might and Magic has the Armageddon spell (whose icon is a mushroom cloud...) it doesn't do that much damage, but it deals damage to everything living on the map; since most NPC's have very little HP it is known as the "Town killer" spell.
Similarly, Heroes of Might and Magic features a spell called Armageddon. It actually can do severe amounts of damage, though not as much as a single-target spell—but, again, the damage is done to every unit on the map, with a few exceptions: the Heroes themselves aren't affected, and any unit immune to fire magic or 4th- or higher-level spells is immune. In addition, units with magic resistance retain their ability to resit it. Finally, in the Armageddon's Blade expansion pack, the titular weapon is an artifact that, aside from boosting the wielding character's statistics significantly, also places Expert Armageddon in the hero's spellbook (regardless of whether they even have the ability to cast such a high-level spell) and makes their units immune to Armageddon. Ouch.
The intro to Heroes of Might and Magic IV shows the result of two extremely-powerful swords (Armageddon's Blade and Sword of Frost) coming into contact with one another. The result is a gigantic explosion with the mushroom cloud seen from space. The world of Enroth is destroyed, forcing the survivors to flee to another world called Axeoth.
Given the two facts that the narrator turns out to be an in-universe character, and that basic facts about several of the campaigns directly contradicts the explosion being that large (we see it immediately cover areas we know had many survivors that weren't immortal), it is probable that the actual explosion wasn't quite so large, even if the clash of the swords caused the end of the world.
The Ultima series has its own Armageddon spell. It empties the planet, save for two or three people, and they are very upset.
In Final Fantasy IX, the summon Odin (in a cutscene) completely annihilated the settlement of Cleyra in a giant explosion.
Same with some final boss animations. *cough* Super Nova *cough*
The well-known "Flare" spell, one of the most powerful ones (excluding summons) in the series, was translated as "NUKE" in Final Fantasy I for good reason; Flare spells are pretty much a magical nuclear blast; whether this is accomplished by magically fissioning atoms around the opponent or teleporting a piece of the sun or whatever is never really specified.
Also; Bahamut. His "Mega Flare" attack is much like any other dragon's Breath Weapon, except he breathes nuclear explosions.
Final Fantasy VI had Merton/Meltdown, which kinda looked like a big shockwave. Fire 3, Meteor, and Ultima make really big explosions, too, but Merton takes the nuclear-weapon-firestorm-and-shockwave similarity cake (if not the damage cake).
Final Fantasy X-2 had Vegnagun, which would supposedly level the same amount of damage as a nuclear weapon.
Its prequel had Sin at this level. It's strongest attack, a Sphere of Destruction, when charged, caused a gravitational pull so strong that it ripped up part of the planet's crust and had a visible effect on the moon, and when fired it moved for miles and left no trace of anything it directly touched.
Final Fantasy VII had the Enemy Skill BETA, which did massive fire damage to all enemies (4000+, and possible to obtain about a quarter of the way through the first disc). The animation was a mushroom cloud.
In-story, the spell Meteor is treated much like a nuclear weapon that had got into the hands of a madman. The phrase Aeris uses for it is even 'Ultimate Destruction Magic', sounding similar to the phrase Weapons of Mass Destruction.
The animation for the Ultima spell in Final Fantasy VIII is a (green) fireball burning the center out of a pure white cloud.
Quest for Glory 5 had the aptly named "Thermonuclear Blast", which does Exactly What It Says on the Tin. Usually, it's just a Non-Standard Game Over, but supposedly, casting it while fighting the final boss results in a Nonstandard victory, where the game mentions that you saved the rest of the world at the expense of Crete. However, the last boss fight can be very glitchy, so using the spell usually just crashes the game.
The Cipher of Damnation is an ancient incantation capable of causing immense damage to a world. In the hands of Gul'dan, it created a massive volcano tainted by fel energy and severed the connection between Orcs and the elements. This may also be the incantation used by the Eredar seen in Velen's visions, which can level an entire world.
Blood elves under Kael'thas developed the Mana Bomb. Early versions didn't damage structures but would kill any sentient beings while irradiating the area. The first such bomb was used to wipe out a neutral outpost, while the second was turned on its own creators.
Garrosh Hellscream has apparently approved its use in warfare. Using the Focusing Iris, a Horde force reduced Theramore to a crater.
The Forsaken Blight is an even better example, a biological weapon first deployed in a Cavalry Betrayal that wiped out a combined force of Alliance and Horde (and even managed to give The Lich King a nasty cough... until he started using it himself). Since then, the Horde have banned using it... a ban the Forsaken don't seem to take that seriously at all. The "weaker" Blights they use are still horrifying and have rendered Southshore uninhabitable by anything except sentient slimes for years to come.
Tales of Symphonia and Tales of Phantasia feature the Mana Cannon. It causes mass destruction (its destroyed all civilization twice, and came damn close to doing so two more times), and leaves vast swaths of areas barren after use, although for different reasons than actual atomic weaponry.
The Heracles' unnamed main gun in Tales of Vesperia is one as well, looking at the cutscene where it's fired and the Pillar of Light that dwarfs the capital city.
The Carronade or Hex Cannon from Breath of Fire IV is one of the more blatant examples seen of the trope. It is powered from the pain and sorrow and despair of human sacrifices who are tortured to the point of insanity first and are explicitly selected based on their connection to the target (yes, you're reading this right; it's a Fantastic Nuke that literally runs on Nightmare Fuel).
One town depicted as being "Hex Cannoned" requires people to go in with decontamination suits for years after its Fantastic Nuking, (although the harmful to all living things magic that fills the town isn't the only problem, as the town is haunted by ghosts created when the Hex Cannon blast kills people and filled with twisted monsters changed by the hex as well) and is depicted explicitly as being uninhabitable for at least a year past that point.
Wild ARMs 2 has a "Nuclear Weapon" being transported that the heros have to stop. It gets released, and it turns out to be a Nuclear Fire Breathing Dragon; which; if not stopped before it takes off in flight; will nuke the country.
The "Reset Bomb" in Kid Icarus: Uprising is a powerful weapon that explodes with the force of a nuclear bomb. What differentiates it from other nukes is that instead of simply laying everything in the blast radius to ashes and ruin, it creates a massive twisting forest in its wake.
The Destroy All spell available to Liches in Dungeon Siege: Throne of Agony. The icon is, of course, a mushroom cloud.
Bring It On Home from Brütal Legend. It summons a flaming Zepplin to crash-land and explode at your location. It's kind of a Wave Motion Gun, you're vulnerable while jammin' out the long and complex spell and it has a five minute recharge.
Master of Magic features the "Call the Void" spell, which sucks an enemy city into the void, with the game effect being much the same as that of a nuke in Civilization.
After defeating the final boss in Phantasy Star III', your character makes use of the otherwise inaccessible "Megido" technique in a cutscene to destroy the final Dungeon Town.
One Expansion Pack for Civilization II features a scenario taking place in the world of Norse myth. The equivalent to the Cruise missile is a lightning bolt, and to the Nuclear bomb is a fireball.
In Dragon Age II, Anders uses some combination of magic and gunpowder (!) to destroy the Kirkwall Chantry and kill Grand Cleric Elthina in the final mission, kicking off the Mage/Templar War.
The Rune Wars in the back-story of League of Legends have some parallels to atomic warfare. Some places are laced with residual magic energy which delivers similar effects to radiation poisoning, for example Kalamanda, the location of the Crystal Scar game map.
The Command & Conquer series typically has actual nukes, but in Red Alert 3, where a Time Paradox led to them not be invented, the Soviets substituted with the Vacuum Imploder. The Allied campaign also depicted a intercontinental laser mounted inside Mt. Rushmore that in game dialogue implies can wipe out entire cities.
Tiberium Wars had a case of a weapon exceeding the power of nuke in the form of the Liquid Tiberium bomb.
The global mode of Universe at War depicts all three sides of the game with their own variant this in the form of their Mega Weapons, which when used on an area automatically kills an enemies on the map without needing a battle. The only one to feature in the game's campaign mode is the Hierarchy's Purifer, and gigantic walker that makes even their usual walkers look small, which they deploy as the final stage of the invasion of a planet to wipe out an remaining life on it.
Guild Wars Prophecies ends its tutorial with the Charr using Titan magic to cause an event known as the Searing. Flaming crystals rained down across the entirety of Ascalon, destroying cities, shattering the Wall, and transforming the idyllic landscape into a barren wasteland. It took centuries for the land to recover from the resulting damage.
Only a few days later, Vizier Khilbron used magic from the time of Abaddon to stop a Charr army marching on Orr. The magic caused the Cataclysm, wherein nearly the entirety of the Orr peninsula sank beneath the waves and every living being was transformed into the undead.
The Lion, a machine specially built to hard-shutdown Europa's most powerful (and craziest) artificially intelligent fortress, has been given something of this treatment as well - it's more like a Fantastic EMP Nuke though.
During her meeting to obtain her spaceship parts in We Are Our Avatars, Imca suggested that Aurora could wipe out the Thalmor with a gigantic magic spell as a warning to those who try to take over the world. At first, Aurora thought it was bad because there's the possibility of civilian casualties. Mitch even compared it to the situation that caused America to drop the nukes on Japan.
In My Little Pony: Friendship Is Magic, Rainbow Dash is capable of a Sonic Rainboom, typically a combination of rainbow and sonic boom. However, as shown in the episode "Lesson Zero", it seems that if she directs the force at the ground, rather than at generating fancy flightwork, it creates a rainbow explosion, complete with mushroom cloud.
In "Twilight's Kingdom Part 2", Twilight creates another such cloud during her one-on-one fight with Tirek. As she is holding the power of four Alicorn Princesses at the time, two of whom are Physical Goddesses, it's pretty Justified.
In the fourth season of The Legend of Korra, Varrick accidentally creates one by tapping into the power of the spirit vines, first accidentally releasing the energy as a concentrated beam and then redirecting the energy into a bomb to destroy all of his work so Kuvira won't weaponize it. Unfortunately, Kuvira's people are able to continue the project, eventually creating a giant spirit energy cannon attached to the arm of a 25-story Humongous Mecha. Similar to actual nukes, Varrick's original goal was to create a source of unlimited clean energy.