Cell planned on becoming one of these after the Cell Games. Once he was finished having his fun on Earth, he planned to destroy it, then travel to other planets and repeat the process. But he was killed before he could get started. His motive was that as the Ultimate Life Form, his true purpose was to cause the end of all life.
Broly blew up an entire galaxy, and nearly did the same to "our" galaxy before the heroes stopped him.
Majin Buu's fat form had no real aspirations of genocide, only killing because he was told to by Babidi and he didn't know it was wrong. His later forms, however, know full well that they're doing evil, and enjoy it thoroughly:
Super Buu lived for two things: challenging fights, and eating sweets. When told to go kill off some humans so as to give the heroes more time to train, he proceeds to launch a storm of energy blasts at the planet below that seek out and kill every last human not on the Lookout save three (Hercule/Mr. Satan, who wasn't targeted because he befriended Buu, and Tien & Chiaotzu, who were able to dodge the blasts). Even after gaining intelligence by absorbing Piccolo and Gohan, he still goes on a destructive spree of blowing up cities for fun (after eating the entire contents ofevery sweets shop in it first), lamenting that the lack of people means he can't enjoy their screams.
Kid Buu is considerably more unhinged, and is pure evil. A simple-minded being, being an Omnicidal Maniac is all he knows or cares about; he blows up the Earth simply because it is there, obliterates several other planets while searching for Goku & Vegeta, and then, once everyone in the vicinity is dead, he breaks into the Afterlife so he can keep killing.
Fall, the ultimate Big Bad of NORA: The Last Chronicle of Devildom' was revealed to be this in the final battle by almost absorbing all of the life energy of the Demon World and the Human World with the insane amount of power he had absorbed from Nora, Duece and the Dark Leige destroying all "defective" beings along with it. All of this out of rage and betrayal towards the previous Cerberus, Diegree, after he died giving strength to the current Dark Leige without fighting Fall a final time. After his defeat, he repents by giving Nora his power back along with the stolen power of the Dark Leige, nearly making Nora a Person of Mass Destruction.
Sir Isaac Ray Peram Westcott from Date A Live claims to plunge the whole world into a endless state of chaos, death and destruction but this is not the only thing that he really wants. His goal in itself is to turn the whole world into a "hell" thus also lead humanity to destruction, without leaving a single life on the planet.
Hellsing: The Millenium's only motive is to cause endless war and destruction For the Evulz, meaning that the war they caused will end if either they get defeated or their opponent, which is humanity as a whole, gets wiped to extinction.
Valgaav, both The Dragon and Big Bad of Slayers TRY wanted the destruction of everything before merging with Darkstar, believing that oblivion was what the world deserved. Afterwards, the knowledge he gained about the nature of the universe drove him to become a Well-Intentioned Extremist merged with Darkstar's godlike power, intending to destroy the entire world and then remake it without strife or conflict.
In the novel canon, all Mazoku are nihilistic Omnicidal Maniacs; in the anime this is most visible with Hellmaster Fibrizo:
Fibrizo: "I want to be destroyed. I want to be destroyed! Destruction? Yes... Destruction is the ultimate wish of any Monster. That's what we were created for. Isn't it? That's what we were created for! [..] But this destruction shall consume all things! It shall consume the entire world! [...] All the world! Let all the world be destroyed with me!"
Subverted with Xelloss, who pays lip-service to the Mazoku "blow up everything" mentality but clearly enjoys life way too much for him to mean any of it. He attempts to excuse his saving the world from Duragnigdu by saying that destroying the world is his job, not Dark Star's. Riiiiight. We believe you.
At that time he wasn't acting for his own benefit, but working as the envoy of the entire Mazoku race, so presumably the surviving Mazoku Lords agreed on his logic there, as well. Plus he was promised that the power released from the killed Dark Star would be granted to the local Dark Lord, Ruby-Eye Shabranigadu. It's left unclear whether that bargain was held or not, but if it was, then Xelloss definitely hastened the homemade Apocalypse by getting rid of the foreign product.
That deal about getting some of Dark Star's energy was never intended to be fulfilled, probably by both sides - nothing shows this more than the fact that Xelloss betrayed the Overworlders shortly after the deal even got mentioned.
Given that most Mazoku fight damn hard to stay alive, it's entirely possible that Fibrizo was simply nuts, and paying lip-service to the cause of universal destruction is the normal attitude of "sane" Mazoku.
Rau Le Creuset of Mobile Suit Gundam SEED isn't perhaps the most obvious, as his goals merely encompass the extinction of humanity, Natural and Coordinator alike. However, given the much smaller scale (the action never extends past Mars due to limited space travel), it's quite omnicidal in context. His motivation for this is that he believes that Humans Are Bastards and have only limped along so far as they have because they have never possessed the means to wipe themselves out before now. He honestly believes that the human race as a whole deserves death, not just for his own admittedly sad life but for all the suffering they inflict upon others that he has seen. Given the atrocities committed by both sides in the war, and the genocidal ambitions of so many in the series, it isn't hard to see his point. In the end, Le Creuset winds up one of the more terrifying examples of this character because his motivations are understandable: it is not impossible to see someone actually winding up with his worldview, rather than just wiping everything out because they're a Card-Carrying Villain.
SD Gundam Force gives us the leader of the Dark Axis, General Zeong. His sole motivation is to become powerful enough to fire a beam that would wipe out all dimensions.
Digimon Adventure has Apocalymon. The name says it all. When he was defeated, he tried to unleash a blast that would eradicate the human world and the Digital World.
Digimon Adventure 02:Big Bad (or so we think at the time) Arukenimon's main plan is to destroy the Cosmic Keystones that maintain the barriers between dimensions, which would cause all dimensions to collide, destroying the multiverse. Her intended Dragon refuses to help on the grounds that she's an unworthy mistress, but eventually decides, for his own reasons, to do the same, making him just as much of an Omnicidal Maniac.
Digimon Tamers features a non-Digimon AI that was designed to prevent other programs from exceeding their boundaries ('cause A.I. Is a Crapshoot) by deleting them if they surpassed a certain stage of development. It decides all humans and Digimon meet criteria for deletion. Then it gets reallynasty.
Digimon Frontier: Lucemon is more of a digital Evilutionary Biologist. The data that makes up Digital World's matter (and population) is easily manipulated, and it all had to be absorbed and used to release him from the Dark Area. He planned to use it to rebuild the world as he saw fit.
Digimon Savers, aka Digimon Data Squad, has Yggdrasil/King Drasil, the computer that runs the Digital World. When the previous arc's Big Bag's plan backfires and both worlds are going to collide, he decides that the human world must go. When the Digimon fight against him and his minions to protect it, guess what he then decides? He, too, plans on restarting the Digital World after destroying the old one.
The Millennium Earl: "You have only witnessed the opening chapter... the akuma in this world will continue to evolve. Now begins the journey leading up to the true tragic end. I am the Millennium Earl, the maker of the akuma. I shall obliterate your puny "God" and lead the world to its death with my akuma. An exorcist, a soldier of life. You can't save this world no matter how hard you try."
The Eclipse virus in Magical Record Lyrical Nanoha Force turns a large number of its victims into a mix of this and extreme Jerkass for some reason, dying horribly if they either cease killing or don't have some sort of medical care keeping it at bay.
Sailor Moon has several, Queen Metaria the Big Bad of the Classic season, Wiseman/Death Phantom the Big Bad of the R season, the entire Death Busters organization of the S season and Sailor Galaxia of the Stars season. Sailor Galaxia, in particular, is notable for omniciding at least a half-dozen, and probably much more, habitable planets, before coming to Earth - by the Grand Finale she wipes out all life in the Milky Way galaxy in both the manga and the first anime. Chaos, who directly controls her and is hinted (or outright stated in the manga) to be the Ultimate Evil behind the rest of them, is one too.
Manga!Prince Dimande became one of these after he was forced to kill his brother and The Reveal of the Big Bad's true identity, going so far as to steal the Sliver Crystals in order to cause the destruction of reality itself. It took Sailor Pluto's sacrifice to stop him.
Many Pretty CureBig Bads were omnicidal maniacs. The Dark King in the original series and Max Heart started the trend by trying to destroy the Universe because it was in his nature; Lord Akudaikahn in Splash Star was his Expy; Dune in Heartcatch was defined by his hatred of everything.
The Director of Eternal in Yes! Pretty Cure 5 Go!Go! is this for worlds he considered to have no value. If a world has a value, he'll drain them of every of its values, that is, treasures. Once they ran out of it, he'll first turn everything of that world into stone, before blowing them up to kingdom come.
Ah! My Goddess, of all series, had one. The Lord of Terror aka The Ultimate Destruction Program, a bodiless entity whose one goal is to destroy the universe and recreate it in its own twisted image. Given the highly idealistic nature of the series, it failed (though it was a close call) and was Killed Off for Real when it was tricked into possessing a floppy disk which Skuld erased using a magnet.
In Mahou Sensei Negima!, the Mage of Beginnings and his minions, the three incarnations of Averruncus, want to destroy Magicus Mundus (a pocket dimension planet the size of and dimensionally anchored to Mars). It's ultimately subverted, as Mundus Magicus is collapsing on its own, and the Big Bad thinks that the only way to save everyone is to move all the inhabitants into a Lotus-Eater Machine.
Yami Malik of Yu-Gi-Oh! explicitly states in the manga that all he wants is total destruction of everyone and everything.
Yuri ofYu Gi Oh ARCV. He explicitly states that he doesn't care about the war he's in, and what he's fighting for. He just wants to defeat and card (essentially kill) people, and wants to card everyone, in every dimension, until he's the only one left. Once he kills Yugo and realizes the power of Zarc is within him and Yuya, he abandons his cause to try absorb Yuya, thus bringing out Zarc and destroying everything.
The Lucifer and Biscuit Hammer has Big Bad The Mage, who is poised to destroy the Earth by hitting it with a giant Biscuit Hammer. His eventual Start of Darkness reveals that he's done this a lot: Being from the future, he has continually travelled backwards in time and destroyed the Earth at every point in time it existed from the point he gained his powers until now. If the protagonists don't stop him he intends to keep on doing this until the Earth no longer exists at any point in time... Simply because he can.
In Noein, Noein's goal is to absorb all possible futures into his own reality, then end the entire universe.
King Zenoheld from Bakugan eventually decided to do this after undergoing a majorVillainous Breakdown, deciding to destroy the entire universe.
Mag Mel entered the picture with this in mind. His ultimate plan is to destroy the Earth in such a way as to set off a chain reaction to destroy the entire universe.
Dewey Novak in Eureka Seven tries to do this by making the Scub Coral exceed to Limit of Questions (the in-universe theory that only a certain amount of intelligent life can exist in a given space, exceeding this limit causes the collapse of the universe)
The second Friend in 20th Century Boys is this. While the first one was comitting genocide with a killer virus for several reasons, he really wanted to be ruler of the world and be worshipped by his circle of "Friends" (all to satisfy his craving for attention and hatred for Kenji). The second one, however, flat out intends to wipe out all of humanity. Despite pretending to be Fukubei (The first one), he really doesn't care one bit about his ideals and doesn't even intend to save those who do support him. He truly wants to destroy the world and his last trap is an Anti-Proton Bomb.
Folken in the movie version of The Vision of Escaflowne wants to destroy all of Gaea — because he's just so depressed and just wants it all to end, even though he presents himself as a Social Darwinist to his followers.
Monster has a more realistic version of this in Johan Liebert, while his motives are left somewhat vague, his actions certainly suggest that his ultimate goal is the complete destruction of human society by manipulating everyone he comes across into killing themselves or each other.
In Puella Magi Madoka Magica, after several timelines of amplified power, our cute protagonist becomes this in her Witch form, Kriemhild Gretchen. She wants to make everyone happy, but thinks the only way to achieve that is by killing them all.
In Riki-Oh, Mukai wants to wipe out the human race because he thinks that is the only way to end their suffering.
Brain's other personality Zero doesn't care for scheming or plans. He's just a powerful nutcase that wants to destroy everything for the sheer hell of it.
Gray: You asshole! You're going to attack a man who can't move? Zero: It matters little if he can move or otherwise. AS LONG AS HE HAS A PHYSICAL FORM, DESTROYING HIM IS WORTH ENJOYING!
Zeref, after constantly being rejected by the world, chooses to reject the world instead and wipe out humanity.
Acnologia. The present storyline has him content with just flying around and destroying stuff and people at random, but Zeref implies that he wants to wipe out the rest of humanity as well.
Togo tries to destroy what's left of the Earth towards the end of Yuki Yuna is a Hero after finding out the Awful Truth about the world. She's a sympathetic variant as she wants to Mercy Kill herself and her friends, stop others from becoming Heroes and having similar faiths, and accelerate the seemingly inevitable demise of the planet. Ultimately, her friends convince her not to go on with her plan.
Downplayed with Grande. He plans to destroy the Human Realm through dark magic in hopes of making a new home for his species to escape the eventual destruction of the Magical Realm.
Jestor from "The Secret of Dragon House" created a computer program to destroy the Witch Realm on the Day of Sleeping. Although he planned to destroy the Warlock Realm as well, apparently he died before he could complete his work.