In The Slayers, the ultimate goal of the Mazoku is to return all existence to Chaos, including themselves. It was most explicitly pointed out by Hellmaster Fibrizo:
Hellmaster: "I want to be destroyed. I want to be destroyed! Destruction? Yes... Destruction is the ultimate wish of any Mazoku. [...] But this destruction shall consume all things! It shall consume the entire world! [...] All the world! Let all the world be destroyed with me!"
In Slayers Try, this is also the goal of the otherdimensional Vorfeed and Dark Star Dugradigdu, supreme Shinzoku and Mazoku of their universe. After realizing how pointless their existence of warfare and endless, cyclic confrontation was, they merged as one entity and went on to destroy the universes created by Lord of the Nightmares as a cosmic Take Thatto their creator. Lucky for them, Valgaav proved the perfect conduit for them in Ceipheed/Shabranigdu's universe...
Folken in Vision of Escaflowne the movie. He wants to extinguish all the misery and suffering from the world by wiping everybody from existence, himself included. His nihilism very briefly appeals to the protagonist who suffers from a bad case of teenager's angst, but pretty soon common sense wins.
At the end of Digimon Adventure, when Apocalymon had his claw-things and the humanoid figure we thought was actually him destroyed, he threw a hissy and decided to nuketify the Human World and Digital World in one shot. The heroes defeated him by standing around going "Oh noes!" until their Transformation Trinkets spontaneously formed a force field in a classic example of Deus ex Machina, containing the blast.
Though most of the Big Bads of Sailor Moon simply want to take over the galaxy, Pharaoh 90 appears to want to completely obliterate the world with The Silence for no other reason than he can.
There's an entire subtrope of Sailor Moon fanfiction as well that takes this route. Typically, someone (usually a rogue band of senshi) decides that destroying the Galaxy Cauldron (where souls are born) will end the recursive nature of war in the galaxy. This would also result in no new souls being born and old souls having no way to be reincarnated, effectively ending existence eventually. In fact, Sailor Cosmos intends to do this in the canon story, and is only persuaded not to do so by Sailor Moon's belief that the beauty of life more than makes up for eternal war.
Neon Genesis Evangelion - It's "only" the eradication of all human life on earth, but Gendo seems to be shooting for that goal. In the end, it's Shinji who triggers it with his suicidal despair.
In Heartcatch Pretty Cure, Big Bad Dune is actually pretty calm and collected. It isn't until he's this close to being purified by their Super Mode that he utterly flips out, grows to planet sized proportions and begins punching the desertified Earth, crying "MY HATRED WILL NEVER BE DESTROYED!"
In Kurt Busiek's Astro City, Infidel narrates that he once destroyed the universe in a "fit of pique." After discovering even that wouldn't kill Samaritan (and Samaritan realizing the same for Infidel), they collaborated to put everything back together. Once that was done, they decided to have lunch together once a year.
Peter David's Captain Marvel (the one with Rick Jones, the latter one) has gone full on looney tunes, mainly because he knows everything. With the assistance of the personification of Entropy (Marvel Comics loves their personifications) Captain Marvel ends all of reality. Off panel. 'Cept Rick, Entropy and the Cap. Rick convinces Entropy to become his 'dad', Infinity and the universe is rebooted.
Lucifer played with this. When informed that he can either take his father's position or let every universe in reality fall apart, unable to get over his daddy issues Lucifer begins an extremely arduous quest to fix the problem some other way.
Fenris is pretty much made of this trope, and Lilith is getting there. She throws a temper tantrum in front of God, demanding him to destroy the universe for putting so much pain in it, while He ponders if he should do just that.
Final Crisis: Once Darkseid is fatally poisoned by the radion bullet, he decides to take the rest of the universe with him, hastening the decay of space-time that his rebirth had already started.
Even post-resurrection, an issue of Exiles had a mission where they had to make sure Jean died, lest Dark Phoenix destroy the universe.
What If #32 ended with a giant Korvac sitting on Earth in a state of bottomless despair, and holding the Ultimate Nullifier. He thinks of everything that ever was, is and will be, and presses the button.
This was a major plot point in Marvel's Secret Wars II, where the Beyonder threatened to destroy all reality because he couldn't find a meaning to existence.
Infinity Gauntlet features a rare non-suicidal Cosmic Temper Tantrum. When Thanos gets angry at Death, he waves the Infinity Gauntlet around, and he sends powerful energy waves throughout the universe which wreck Earth.
Azrael, the mastermind behind the plot of Dogma, fits the bill. Being trapped in Hell forever is a pretty compelling motive for wanting to undo existence. He also claims that since he didn't fight on either side during Lucifer's rebellion, he should not have to suffer the same fate as those who DID fight God.
By about halfway through the final battle of The Avengers, it's pretty obvious that Loki doesn't actually care about subjugating Earth anymore and is just reveling in the destruction he's wreaking, with little to no concern for himself anymore. Right up until the Hulk beats him six inches into the floor.
In Life, the Universe and Everything, the people of the planet Krikkit live on a planet surrounded by a totally opaque dust cloud, so for centuries, they know nothing of the universe beyond their planet and the star they orbit. When a spaceship crash-lands on the planet, they use it to take an exploratory trip, curious of where it came from, and see the universe for the first time. Their immediate reaction? "It'll have to go." Later revealed to be due to the influence of a supercomputer which had been commanded by its programmers to build the ultimate weapon. It needed them to help him use it, and enhanced their war efforts.
In Guy Gavriel Kay's The Fionavar Tapestry, this is the motivation not so much of the Big Bad as of his Dragon. The reason? Long ago, he couldn't get the woman he considered his One True Love (she went with a mere human instead, who became Fionavar's first wizard) and swore an oath that he would end the world that had witnessed his rejection; how and whether he's planning to survive at all if and when he succeeds isn't clear, but towards the end of the trilogy he gets the chance to try. He fails, though only through the timely arrival of the one character who can stop what he's just unleashed — and in the process learns to his own surprise that he's not yet beyond redemption himself.
In The Courts of Chaos (book 5 in the The Chronicles Of Amber), a giant tries to convince Corwin to stop trying to save the multiverse. Corwin, of course, refuses to give up.
The alternate dimensional beings in Michael Swanwick's Jack Faust have the capacity and intention to survive until the heat death of their universe, but not beyond; they can observe and communicate across realities but can't physically leave. Because of the massive difference between how time flows in the two universes, their universe will end in several hundred to several thousand of our years. These beings find humanity so offensive that they assist the titular character in an effort to totally wipe out the species - the mere idea that humanity may continue to exist after they no longer do is a terrible affront to them.
Utuk'ku, the Norn Queen in Memory, Sorrow, and Thorn, is the oldest living being in the world, and wants to drag as much of the world as possible with her into death.
Subversion: The villain in the fifth Spellsinger novel harnesses a transcendental creature, and Clothahump assumes he intends to destroy the world with it as a grandiose form of suicide. As it turns out, though, Braglob did it For the Evulz and had no specific plans for the thing at all.
This is the ultimate fate of the universe in Harlan Ellison's The Region Between, destroyed by the same insane God that made it, who kills himself in the process.
In The Wheel of Time, this is Moridin's ultimate goals. He's a nihilist who is one of the few characters to be really Genre Savvy about the Eternal Recurrance of the Wheel, but can't concieve of it as anything but a cause for infinite, pointless suffering and misery. He's also a Death Seeker in his own right, but Wo T's 'verse features reincarnation as a central element, so if he dies, he'll simply be born again. The solution? Willingly submit himself to the Dark One, the only being who has the power to destroy him and the world for good, and help him escape his can so that he will destroy reality, and Moridin with it.
In a fourth season story from Doctor Who, "The Underwater Menace", Professor Zaroff, embittered because his wife died in a crash (at least in the original script), has the goal of making a hole in the seabed under the Atlantic so the erupting lava would boil away the ocean, destroying the Earth. Only the Earth would be destroyed, not the universe, but it still pretty much counts.
Davros' "reality bomb" in the new series must count. Apparently, he got tired of world/galaxy/universe domination and decided that completely destroying reality was the real pinnacle of achievement.
Tharizdun from 3.5 and earlier fits this trope to a strong degree, except his exact reasons for wanting to annihilate all existence aren't ever explored.
He's the god of destruction. It's his job.
He went mad after touching a shard of Pure Evilness(tm), which may or may not be the only remains of the previous universe.
The Deathlords of Exalted all have the canonical aim of 'being the last person there to blow out the candle of creation', in direct service of their Neverborn Masters. This also presumably extends to any loyalistAbyssal Exalted. Mind you, for the Neverborn, this isn't so much "wiping out the world because it won't have me" as it is "someone, please just pull the plug" — they can't die because their souls are bound to Creation, so they're just caught in an endless state of agony.
Rovagug from Pathfinder wishes to destroy absolutely everything. He has no allies in the cosmology at all, to the point where if he were to be released, EVERY SINGLE SOLITARY GOD would stand against him.
Dimentio falls back on this plan after his One-Winged Angel form is defeated (his original plan was remaking everything in his own image, his last resort was to leave the Chaos Heart/Void going and take everything out with him).
Kuja in Final Fantasy IX is a true example of the "temper tantrum" part of the trope and probably the best example from a Final Fantasy game. Upon discovering he's a mortal and is an Artificial Human who's due to expire any day now because he was only a temporary pawn, he decides if he doesn't get to live, why should anyone else? He's so selfish and arrogant he doesn't think it's fair that life will continue after he's dead.
Neo-Exdeath from Final Fantasy V wishes to draw everything into the Void, and then disappear himself. This isn't out of anger like Kuja; it's just what he does.
What Straw Nihilist Kefka wanted to do in Final Fantasy VI, although it was never clear whether he intended to destroy himself afterward. Dissidia: Final Fantasy implies it's because he's unable to understand the point of life, thus he wants to destroy everything because everything else is meaningless to him.
Final Fantasy X: Implicit in Seymour's Evil Plan—he views death as a wonderful release from the suffering of life, hence everything deserves the so-called mercy of dying. However, given the weird way death works in Spira, it isn't that he wants to destroy everything for the sake of destroying it, Seymour actually thinks death is a step up from life—death didn't much slow down Auron, Yunalesca and Seymour himself when they died, and Yunalesca has been dead for 1000 years. Of course, that's not to say his plan was well thought out, because killing everyone in an apocalyptic fashion would probably cause them to become Fiends, as they would die painful, horrible deaths.
The focus behind the Twist Reveal in Final Fantasy XI with the Chains of Promathia expansion where it is revealed that all beings on Vana'diel are parts of the Twilight God Promathia, and his belief that destroying all those loose parts of himself are the only way he can die and free himself of the pain of existence.
Dissidia: Final Fantasy, Chaos decides to tear apart the combined realities that make up the battlefield for the conflict of the Gods, and then disappear himself. Its due in part to just being sick of the endless cycles of conflict, death, and rebirth, and in part because Cosmos' death has triggered a My God, What Have I Done? moment for him when he realized they used to rule together in peace before the wars began.
In Crisis Core: -Final Fantasy VII-, Genesis Rhapsodos falls under this when Dr. Hollander says no one (not even Dr. Hojo) knows where the Jenova cells are, which is what Genesis is looking for. But Dr. Hojo does know.
The Legend Of Zelda Majoras Mask. The titular mask contains a quite lunatic and uncontrollable spirit that thought it'd be a hilarious prank to destroy the world by making the moon collide with it. Even the moon doesn't like this idea!
Ghadius from Klonoa: Door to Phantomile attempts to destroy the world as revenge for being sealed away 3000 years ago. He doesn't care that his plan would destroy him along with the rest of Phantomile.
The King of Sorrow from the sequel appears to be attempting the same thing, as by linking the Kingdom of Sorrow to Lunatea is implied to cause some degree of destruction.
Diablo: According to the Diablo I manual, the minions of Baal, the Lord of Destruction, seek the undoing of the universe.
In God Of War: Chains of Olympus, Big BadPersephone hires the Titan Atlas to use the kidnapped sun god Helios' powers to destroy the pillar that holds the world up, causing it, Olympus, and the underworld to crash down on top of each other and kill everyone. It's a form of suicide-revenge; she's tired of living in a loveless marriage to Hades, and wants to get back at her husband and Zeus for trapping her in it, believing The End of the World as We Know It to be a fitting way of solving both problems. she doesn't seem terribly happy about it, but she just cannot take it anymore. It's the first hint at just what an enormous bunch of dicks Kratos is dealing with here
Live A Live, the Armageddon Ending, triggered as a menu command.
Mother 3, (mega end of the game spoilers) As a result of his time-traveling, immortal body, and countless years of life, Porky has grown supremely impossibly, crushingly bored with all of creation. So he plans to have the Needles sealing away the Dark Dragon pulled to destroy what little there is left of the world, and live alone forever, just him and the Dragon.
Disgaea 2 can end with Laharl destroying the world in a pique, or Rozalin dead, but Adell possessed, and he not only slaughters his own family, but it's strongly suggested that the rest of reality will soon follow suit
Then played very muchNOTfor laughs in the Demon Path. If you win the final battle, Revya kills both Haephnes and Drazil and erases both their worlds from existence, killing everything on them and him/herself with it. Any last words as they lament the destruction of everything with their dying breaths? Oh yes:
If you can untangle the Mind Screw of a plot, the Time Devourer from Chrono Cross is basically undergoing one of these. After the canon ending of the original game, the resident Eldritch Abominationabsorbed Princess Schala, and the influence of a conflicted human intelligence warped Lavos's simple, mindless hunger into a desire to destroy everything to wipe the universe clean. When you fight it as the final boss, it's in the process of absorbing all of time and space, leaving it alone in the abyss. The only way to permanently stop it is to use the titular Chrono Cross to separate Lavos and Schala.
In Webcomic/Goblins, an alternate-universe version of Minmax is one of these. He finds his way into a side universe (along with some of the main characters) and promptly sets in motion a plan to make it so that he, along with the side unierse and everyone in it, never existed.
Note that not only does he have a Punny Name, his plan would have worked brilliantly if the Spanner in the Works main characters din't show up, and through their actions, destroy the Punyverse. How do they do it? By stealing the crotch ofGofotron, letting a small puppy detonate every sun in the Punyverse.
Parodied in Earthworm Jim. Evil the Cat wants to destroy all of creation. When someone asked him what he would do afterwards: "Gloat, I suppose."
In Ben 10 Alien Force, this turns out to be the plan of the Highbreed; they're going to die out within a generation due to inbreeding and subsequent genetic problems, so dammit, they're going to take every other species down with them.
This is what the Shredder's plan in Turtles Forever boils down to, a course of action he chooses to take after discovering the truth about the multiverse. He's torn on whether or not killing the Turtles was worth dying himself but in the end, he thought it was totally Worth It.
That's not what Word of Faust says. Her comment on the issue was that Nightmare Moon, had she succeeded would have ushered in "an era of evil"...meaning that life would have continued much as it did during Narnia's eternal winter. Albeit with a lot of pony-eating monsters.
In Squidbillies, God's equally-omnipotent stepbrother blows up the world out of nowhere because he was angry about being The Unfavorite.