Cars from JoJo's Bizarre Adventure (the page picture above) wanted nothing more than to help his race overcome their weakness to sunlight and "conquer creation", thereby becoming the most powerful creatures to have ever existed. However, as he needed to sacrifice an insane amount of living beings in order to do so, and his fellows weren't interested in running roughshod over the world in the first place, they eventually turned on him and he was forced to kill them all in self-defense.
Fate Averruncus's organization in Mahou Sensei Negima!. To the point it's questionable whether his goal is actuallythat bad, and the protagonists are simply opposing the means he's using to bring about that goal.
His true ultimate goal is "saving" the Magical World (which will soon suffer complete magical depletion) through an Assimilation Plot, and he progresses towards it: 1-without informing anyone but select coconspirators about the true plan, playing the rest as Unwitting Pawns, 2-by engineering wars, unrest and disasters that cause untold suffering on a massive scale, 3-Stopping at nothing to neutralise anyone who might pose even the slightest threat to his plans, even if that "threat" is the possibility to find out how to Take a Third Option where nobody dies. He's a prepubescent Gendo Ikari.
In Drifters, the Black King seeks a world without humans. Which he intends to create by annihilating them and teach the magical creatures how to live in society, giving them religion, knowledge and the means to survive in a single, unified front.
Ribbons of Gundam 00 who sees himself as the benevolent god who lead humanity into a utopia and prepare them for contact with aliens.
Quite common in Gundam series, dating back to Gihren Zabi in the original. People like Anavel Gato, Char Aznable, Treize Khushrenada, and others fit this trope perfectly. Anavel Gato chews out Kou for not bothering to understand Zeon's objectives and mindlessly serving the Federation. Char has a very well-organized and detailed ideology he inherited from his father and resents Amuro Ray for not being similar ("Unlike you, I'm more than just a pilot!"). Treize, especially, has a vision of the glories and terrors of war and wishes to drive home to humanity the true horrors of war...but due to his suicide-through-enemy-fire, he escaped responsibility for his actions. Considering that Treize was RIGHT in his ideals, but not his methods...
Both Pain, Obito and Madara of Naruto have clear goals and plans to achieve the utopia they envision. The first wanted to create a system similar to the Cold War doctrine of Mutual Assured Destruction, while the latter two veer more towards a standard Assimilation Plot. As the plans of the former two were mutually exclusive, they danced around each other, trying to advance their own goals faster. Whether or not Madara's claims towards his ultimate goals are to be believed is a matter for some debatable.
Despite an abundance of dickish villainswho do their devious acts on a whim, One Piece surprisingly has one in the form of Hody Jones. He wants to restore Fishman pride, with his crew, The New Fishman Pirates, by fostering hatred between the people of the sea and those of the land: humans, by assassinating Queen Otohime, the greatest advocate for peace between fishmen & merfolk and humans, and using a human as a patsy, planning to kill King Neptune for his perceived "weakness", which is allowing humans to protect the island (e.g. Whitebeard, Big Mam), have his crew terrorize people who help humans, and after he takes over the kingdom and purges Fishman Island of "human-loving trash", he planned to enslave humans across the oceans, before setting his sights on becoming Pirate King.
Jinsuke Kurogame from Gamaran. He's one of the greatest swordsmen in the world, and created his own martial art school (the Muhou Ryu), composed of strong warriors from many different styles. His plans involve take over Kyushu and turn it into an independet nation, and then use it to challenge the Bakufu, conquer the rest of Japan and turn it into a country of warriors where strength and power are the most important things.
Griffith from Berserk. A peasant boy turned mercenary who dreamt of having his own kingdom, at least in part due to his hatred of the current nobles and class-based social hierarchy. This one has since Gone Horribly Right, in that he achieved his dream, ultimately, but at the cost of sacrificing his closest friends to demons during the eclipse.
Griffith's a... complex example. Pre-eclipse he wants to overthrow the current class system, not so much because he thinks that such systems are fundamentally flawed, but because he thinks there's been a mistake in exactly who should be sitting on top. (Spoiler: he thinks it's him.) At best you could say that he's in favor of upward mobility as opposed to true equality, at worst he's simply self-serving and narcissistic. Post-eclipse his rule seems largely benevolent so far (discounting what hehad to doto get there), but it's unclear whether this is how he intends to run things long-term or if he's just cultivating a good public image until he can solidify his rule. So while he very well may be this trope, he might also simply be a power-madPragmatic Villain who's found that a reputation as a visionary best serves his purpose. He's playing a long game, and his ultimate goals are still largely unclear.
Aizen from Bleach. Although his initial motivation seems to be primarily Despotism Justifies the Means with a dash of For the Evulz, the end of his fight with Ichigo suggests a deeper motivation concerning a disgust with how the Soul Society is run; especially in regards to the role (or seemingly lack of one) played by the Soul King; claiming that just accepting the world as it is like Urahara told him to be the mentality of the weak while the strong force the world to conform to their ideals.
Watchmen: Ozymandias slaughtered half of New York, killing millions, in an attempt to save the rest of the world from a nuclear apocalypse.
Magneto, at his most Anti-Villain, wants only to prevent mutantkind from undergoing the same persecution he did in WWII. Sometimes this means creating a private island / satellite for mutants, other times it means actively subjugating the human race to ensure they will never be a threat.
Doctor Doom believes to the very core of his being that what he's doing is right. He's looked in the future (His words) and only saw one potential future where everything ends up well, and that's under his reign, as per Doomwar.
Likewise his Ultimate Universe counterpart Is NOT this trope, but in fact Ultimate Reed Richards is!
In the Jackie Chan Adventures fic Queen Of All Oni, Jade's goals are simply to gain power so she can do as she pleases, and to prove to Jackie how she never got the recognition she feels she deserves from all the times she helped him in their adventures.
The Villain Protagonist of the Mass Effect fanfic The Council Era, a salarian known as Tyrin Lieph, dreams of uniting the galaxy as a singular utopia. His Worthy Opponent Halak Marr seeks to overthrow the Citadel and establish the krogan as a sole-surviving Master Race. Their conflicting visions eventually erupt into the Krogan Rebellions.
Loki, Big Bad of My Little Avengers. While he may appear to be doing things For the Evulz at first, it's eventually made clear that he has a vision of a world ruled by magic (preferably with him in charge, natch), and the entire plot is revealed to be one big Gambit Roulette dedicated to bringing this goal about. When he's defeated and killed, he still manages to die happy, knowing that the magic released by his death will permanently mutate Equestria, bringing his vision to fruition.
Whereas in canon he was the poster boy for Hidden Agenda Villain, Jewel Of Darkness turns Slade into one of these. He firmly believes that the mounting tensions between the normal governments and the superpowered factions (good and evil) will lead to World War III, and that the only true victors will be those who have gathered enough influence and reputation to become leaders in the devastated world afterwards.
Fallen King has Pegasus, who gleefully explains his plan to reshape the world in his image and to his rules.
Dr. Octavius in Spider-Man 2 refuses to give up his dream of creating fusion-based electricity for "the good of mankind." Too bad his generator always explodes upon activation. And he plans on making an even bigger one when the first one blows up.
M. Bison in the live action Street Fighter film wants to create a race of genetically-engineered Super Soldiers to wipe out all traces of race, nation and creed so that the whole world can live in peace under his rule.
In The Dark Knight, everyone thinks that The Joker is "garbage who kills for money", or just a homicidal maniac who kills for kicks. However, he is adamant he has grander ambitions- he is out to give the city "a better class of criminal" and sees himself as heralding a new age of supervillainy, as well as working to expose the citizens of Gotham as just as bad as he is.
Not necessarily supervillainy as much as chaos. He wants to tear away the veneer of civilization and watch everyone abandon the moral order they claim to value so highly.
"I'll show you. When the chips are down, these... these civilized people, they'll eat each other. See, I'm not a monster. I'm just ahead of the curve."
Both Ra's Al Ghul and Bane and Talia from the first and third movies qualify, as well. Ra's sees the human race as inherently decadent and corrupt, with the League of Shadows acting to destroy the most significant sources of these sins at their zenith, the current target being Gotham. Considering what we see of the police force and general apathy of the citizens he's not entirely wrong. Bane wishes to complete his vision though more dramatically, including literally showing Gotham how awful it is as even its strides towards peace and order between movies seem to be built primarily on lies and cover-ups. When it shows later that he's merely The Dragon for Talia, and both actually want revenge for what happened to Ra's in the first film, how strong their visions remain and how much they're just used as an excuse to blow up Gotham is called into question.
Judge Doom from Who Framed Roger Rabbit made a surprisingly epic speech about his grand Earth-shaking vision of public freeways. His plan does require Toon Town to be wiped out first.
Sebastian Shaw from X-Men: First Class, who wants to start World War III so that mutants can take over the planet.
Though in his case it's because he's just in it to Take Over the World, with little actual regard for allowing his kind to thrive (he merely uses it as his rhetoric to recruit others). As above, Magneto is much more suited to the trope, even going so far as to applaud Shaw's vision of a mutant-dominated world but in exactly those terms, without the desire to rule over them as their supreme leader.
John Harrison/ Khan's speech about how the Augments were created to lead others to peace in a world at war.
Admiral Marcus, who wanted to create a more militarized Starfleet in preparation for what he believed to be a looming war against the Klingons.
A variant: In The Protomen's album The Father of Death, Drs. Light and Wily work together on a massive automaton network, ostensibly so that everyone would be safe, secure, and not have to worry about dying on the job. Wily's the one who ultimately gains control of the network, ruining Light's reputation in the process. Light realizes that creating the network was a mistake...
"They've waited so long for this day / Someone to take the death away / No son would ever have to say / My father worked into his grave..." - Dr. Light, The Good Doctor
Mega Man music projects seem prone to this: one of Wily's goals as told by The Megas is to replace humans with robots, which he believes are superior.
Given that there has never been a canonical life expectancy for Chiss, people will still be expecting Thrawn to show up long into the future.
In the Everworld series, most of the villains are short-sighted hedonists who avert this trope, with the definite exception of Senna Wales, who has big plans for Everworld and very definite ideas of what she is going to do to it.
In the BattleTech novels, Visionary Villain types are quite different than those that amass power for it's own sake. The bigger heroes generally do things for the good of humanity overall, lesser heroes and some villains generally grab power for their own nation or group, and the real big villains are just in it for themselves. Examples:
Hanse Davion fought several wars against the Draconis Combine and cut the Capellan Confederation in half. He always saw himself as striking against oppressive regimes run by madmen (Which was true, in the case of the Confederation. Debatable in the case of the Combine). He also saw himself, like many Successor State lords before him, as the fittest candidate for the 300-year vacant title of First Lord of the Star League. He was depicted as a scary man to be against, though with good intentions.
Sun-Tzu Liao was willing to do terrible things, but his foremost goal was rebuilding the Capellan Confederation after Hanse broke it and Sun-Tzu's crazed mother all-but-destroyed the remnants. He was generally depicted as villain and very dangerous, but one who's position was understandable and not nearly as bad as some.
Sauron started out this way, determined to create peace and order on Middle-earth at any cost. Over time, though, he suffered Motive Decay and became a straight-up tyrant (The Dark Side Will Make You Forget is a recurring theme with Tolkien villains). Sauron's path to villainy is later repeated on a smaller scale with Saruman.
Bigger Bad Morgoth, as well. Back at the very beginning, he just wanted to create a world of his own imagination, and when he found that impossible, settled for wrecking up the world that was actually created.
Tigerstar, the main villain of Warrior Cats is one. He dreams of ending the constant war and uniting the four Clans as one, entering a new age of prosperity as a result. Of course, his ego makes him believe that he is the one suitable ruler of this combined Clan, and it leads him down a dark path in his struggles to create it. Hawkfrost, Tigerstar's son from the Sequel SeriesThe New Prophecy follows his father's vision, but is just as egotistical as Tigerstar.
On Homeland, terrorist mastermind and Big Bad until he was finally killed Abu Nazir had a very long-term plan to eventually destroy Western Civilization, admitting that it might take centuries and many lost lives on both sides but envisioned his side winning in the very long term.
Arrow: Season 1 Big Bad Malcolm Merlyn/Dark Archer has the Undertaking, a plan to "save" the city by destroying the crime-infested Glades, not caring that it will kill hundreds (if not more) in the process.
Khan Noonien Singh of Star Trek was once "the best of tyrants" ruling a quarter of the human population and in the AU story "Seeds of Dissent" (part of the Star Trek: Myriad Universes) presides over the genetic transformation of humanity into a Superior Species after his successful conquest of Earth. In the episode "Space Seed," upon his defeat, he gladly accepts the offer to tame a new world.
Some leaders in Warhammer 40,000 are fighting for a strengthened humanity able to endure the grim darkness of the far future...united under the eight-pointed star of Chaos. Others, however, just want something, and the difference is often academic if they're offering you up to the Dark Gods or raining siege shells on your city.
The Clans in BattleTech count, they see themselves as the chosen descendants of Kerensky, and believe its their right and destiny to conquer the Inner Sphere and rebuild the Star League. But each of the Clans have conflicting views and they don't always agree on anything, and their rule is simply a caste based military dictatorship which benefits the warrior caste only, and their culture mostly favors Trueborns and treat Freebirths like dirt.
Seymour in Final Fantasy X is a subversion. He thinks he's this because he wants to end the cycle of life and death on Spira. However, the whole party calls bullshit on it because he very clearlyenjoys being a horrible bastard and his method of ending said cycle involves killing everyone alive. He doesn't have much of a counter-argument.
Interestingly, a bit character from the X continuity, Rin, is a more straightforward example. By the time of X-2, the Al Bhed are busily re-introducing robotics and machinery into society. Rin decides that the machines can work in unison better than a human workforce can, but his faulty programming causes them to run amok. (note that this only happens in his scenario; there are four possible culprits, and only two of them are truly malevolent.) When confronted, he gloats that he intends to continue covering up accidents and won't rest until Spira is a fully-mechanized society — presumably with himself at the helm. This is a little chilling since the character had carefully hid his ambition up this point.
Cyrus from Pokémon Diamond and Pearl, who wants to destroy the world and then re-create it as a world with no emotion, knowledge, or willpower, claiming that these things that make up "spirit" only lead to pain and conflict.
N wished to free all Pokemon and create a world where Pokemon wouldn't be enslaved. A lot of Team Plasma shared that vision with him.
In Ruby, Sapphire, Emerald are Teams Magma, and Aqua who both are motivated to do what they think is best for the world. By controling Groudon and Kyogre to make more land/water respectively.
Kerghan in Arcanum might be the most well-intentioned and extreme extremist of all. He's traveled beyond the veil of death and knows it as plain fact that the dead eventually do reach a state of perfect tranquility in death. Since he's all too aware of how much the living and the undead suffer, his grand scheme is to permanently sever the mortal ties of every soul in existence. He's quite insane, but there's nothing in the story that indicates that things wouldn't work out exactly as he'd foreseen if given the chance.
In the end, you have the option of joining him and helping him to kill every living thing in existence. Whether or not this is the bad ending isn't quite made clear.
BioShock has Andrew Ryan. Some of the other old holdouts down in Rapture count in their respectivefields. Though Ryan takes the cake for building an underwater city for purely ideological reasons, going to rather ludicrous ends to preserve it, and fully planning to build it back up to its glory days again even after its become a leaky, ruined mess.
Sofia Lamb in the second game has opposite goals (the foundation of a collectivist society).
In Infinite, we have Zachary Hale Comstock and his vision of creating his own heaven in the form of Columbia. And that's nothing compared to what he wants to do to the "Sodom Below"....
From the first game, Saren began as one ( seeing the victory of the Reaper machines as inevitable, he was trying to prove that organics served some constructive purpose, so that there would be a "logical" reason to spare some of them, and thus prevent complete galactic extinction) but the subtle yet continuous Mind Rape inflicted on him prevented him from realising three things; 1. The Reapers were not actually invincible, and it was possible to have a chance against them. 2. The reason for the Reapers purging all advanced life (revealed in the third game) meant that no logical purpose was served by keeping him or any other organics alive. 3. He was completely indoctrinated so it wasn't his vision he was implementing. By the time of the final confrontation he's simply become Brainwashed and Crazy.
Played with in that we never find out exactly what his vision (as separate from the visions he presents to his followers) is. Clearly, he has a plan, but it seems to result in wildly different goals between one game and another (exactly what is the connection between Divination and Ascension?).
The Master in Fallout 1. Believes that his Super Mutants are the natural evolution of mankind and the perfect solution to the irradiated, destroyed Wastelands of 22nd-century California.
Caesar from Fallout: New Vegas. He thinks that the post-apocalyptic earth is proof that democracy has failed, and sets out to unite what's left as a monotheistic dictatorship, replete with slavery, crucifixion and institutionalized sexism (including legally-sanctioned rape). At the game's beginning he's conquered Arizona, Utah, New Mexico and Colorado, and is poised to take Nevada.
Benny's goal is revealed to have been to take control of the Securitron Army and overthrow House, allowing him to create an independent New Vegas free from the NCR and Legion. In the Wild Card Ending, the Courier takes up where he left off and proceeds to do just that.
Jacques the Aldersberg, the Grand Master of the Order in The Witcher.
The Ur-Quan Kzer-Za from Star Control II believe that enslaving every race they meet is in the service of the greater good. The Kzer-Za are protecting themselves from potential threats in these other races (they had a bad experience) and protecting their slaves from their Omnicidal Maniac cousins and possibly other, more sinister threats as well. Any slaves who resent this treatment just aren't seeing the big picture.
In Dragon Age, the Architect in Awakening is explicitly referred to as being this by Velanna after the reveal that his "Evil Plan" was to use Grey Warden blood to sever the Darkspawn's connection to the Archdemon, with the sole intention of granting his brethren intelligence and self-awareness, rather than trying to rule over them. The Warden can admit his plan could lead to peace and can choose to ally with him.
Weijuaru of Juathuur uses his position as king — a position the juathuur are never allowed to take — in order to give juathuur deserters a place to be free of Meidar and to find a way to travel to the other worlds the gods have made. When you find out how much of a Control Freak and Manipulative Bastard Meidar is, the "Villain" part gets dropped.
Redcloak, The Dragon from The Order of the Stick, is motivated by a vision given to him by his God, of goblins being able to be equal to the other races and building their own proper society and civilization instead of scratching out a living in places none of the other races would want to live. And if one potential consequence of the plan to accomplish this is the unmaking of reality as it currently exists, well, it's all for the greater good, right?
Tarquin as well. He runs a conspiracy to control the three most powerful nations on the Western Continent in order to bring it to peace and himself to absolute power
Skitter of Worm eventually develops into one of these, taking over a city's criminal underworld on the grounds that she can make it run more efficiently and with less violent crimes or drug addictions if she's in charge, and creating alliances with other supervillains that mandate their aid to fight the Endbringers.
Lord Doom, from the Global Guardians PBEM Universe, wants to take over the world because he is a Holocaust survivor, and doesn't want to see another child go through what he went through. Along the way, he plans on improving the health and standards of living for everybody on Earth.
Although his vision is not clearly revealed, Chase Young from Xiaolin Showdown fits this trope.
Nerissa in the animated series and comic W.I.T.C.H., who betrayed her teammates and later attempted to conquer the universe, claiming to seek an end to all war and conflict.
Fire Lord Sozin wanted to "share the Fire Nation's prosperity with the rest of the world." This ended up involving the betrayal of his best friend, the invasion and colonization of the Earth Kingdom, the (near-)complete genocide of the Air Nomads, and raids against the Water Tribes. This "Great March of Civilization" remains the Fire Nation's propaganda, but Sozin's grandson Ozai just wants to rule the world even if it's nothing but ashes.
Aligned Continuity Megatron. Though he originally wanted to bring an end to the caste system that kept Cybertron infested with political corruption and social inequality, Motive Decay eventually set in and Megatron's new goal became rebuilding cybertron in his own image where the strong ruled without question.
In contrast to the rest of the Light, Klarion is in it For the Evulz.
We see a particularly impressive example in Justice League: Crisis on Two Earths: While the Injustice League of the parallell dimension mostly consists of superpowered thugs, Owlman is another creature entirely. Upon finding out about the existence of the multiverse he comes to the conclusion that free will is an illusion as every choice we make is countered in another dimension. He decides that this makes his and everyone else's existence pointless and in the matter of days put together a plan that will let him annihilate all life in all parallell dimensions that exist. He considers this act the only meaningful one he can make as it is truly unique and can only be done once by one being in all the multiverse.