In Jackals, Lee Mei Lang is so skilled and awesome in her absolute villainy that you can't help but root for the total bitch she is.
Even better, the reason she took over Tennouren to begin with was to destroy every gang in the city including her own. All in order to essentially gain an ARMY * and create a town that isn't ruled by gangs but mostly to gain an army. To wit, she and her spider-whip henchgirl are the only people to walk away from the gang wars completely unscathed.
Series protaganist Rock seems to be turning into a anti-heroicMagnificent Bastard as he becomes steadily more jaded. Whilst he's manipulating everyone around him and with a Slasher Smile that tells you he's thoroughly enjoying himself, is that his goal is ultimately to save as many lives as possible.
He talked back at Balalaika and lived. That alone shows how much of a Magnificent Bastard he is.
Let's not forget Balalaika's biggest Rival and pretty much the only mafia leader in Roanapur who can more or less constantly keep up with her: Mr. Chang from the Kan Yi Fan Triad.
With the latest OVA series it is clear that Chan and Balalaika are equals. Balalaika might have her absolute lead in prowess and wit, but Chang makes it up with his great influence and far superior contacts, with CIA for example.
Aizen fakes his own death and fools all of his former superiors and former subordinates, takes over the world of hollows, and plays the Large Ham role to its finest when he undergoes multiple transformations that drastically increase his own power. All to obtain the Plot Device that'll help him enter the realm of divinity. However, towards the end, he becomes so reliant of the Plot Device to increase his power to the level required that Ichigo overpowering him causes him to melt down in a Villainous BSOD. This allows him to be defeated by Urahara.
Shukuro Tsukishima manages to brainwash Ichigo's entire family and everyone he knows and cares about. He then outgambits Byakuya Kuchiki by using the petals of Senbonzakura to take control of Byakuya's memories, inserting himself as Byakuya's combat mentor so that he knows every single one of Byakuya's fighting abilities and strategies. Unfortunately, Tsukishima didn't bank on Byakuya's Pillars of Moral Character nature hiding both an Undying Loyalty to Ichigo and such a secret inner Blood Knight instinct that even Byakuya didn't know he possessed one.
Yhwach sends an emissary party to Yamamoto informing him Soul Society will be at war in five days that consists of Yamamoto losing half his entire division in three minutes. Less than 24 hours later, his army invades, taking out more than half the Gotei 13 and multiple captains and lieutenants. He also kills Yamamoto by exposing Yamamoto to doombot that manages to draw out Yamamoto's bankai. Once Yamamoto's power is exposed, Yhwach is able to steal it and kill Yamamoto. He's also carefully implanted soul fragments in all of the shinigami that have fought quincies, allowing to feed off their power - when any individual dies, Yhwach gets stronger: so every time the shinigami win a fight, they're actually losing.
Minister Foss in Berserk. And from his perspective, Griffith.
Code Geass: Lelouch of the Rebellion is full of these, with the Anti-Hero Lelouch being one of the best examples ever. He turns a weak regional rebellion into a massive world war against his father, all while under the guise of the fabulouslytheatricalmasked persona, Zero. His older brother Schneizel lacks the theatrics, but more than makes up for it in sheer competence, managing to wipe out all the progress that Lelouch made in over forty episodes in less than four minutes - though admittedly only through Lelouch's inability to kill an unarmed enemy soldier 40 episodes prior, and his unwillingness to use his Geass to erase knowledge of the Geass Research Facility. Without that, Schneizel's words would have just been hot air.
Even when Schneizel separates Lelouch from the Black Knights, Lelouch manages to go and take over THE OTHER HALF of the world and goes on to finish taking over the rest of the world that he'd previously lost. His Magnificent Bastardness REALLY shines through, however, when you realize that taking over the world was really just part of a bigger plan to create a peaceful world for his precious sister Nunnally.
Cell from Dragon Ball Z: In his imperfect form, Cell runs rings around the Z fighters as he masterfully evades their attempts to ambush him while draining countless cities of their population's bio extract. Upon finding himself sorely outclassed by Vegeta later in the series, Cell tricks the Saiyan prince into allowing him to absorb Android 18 by promising to provide him with an opportunity to test the full extent of his newfound power. In the ensuing rematch, he succeeds in reaping vengeance upon Vegeta by breaking him down physically and psychologically. He then more or less toys with the Z-Warriors by forcing them to play by his own rules in the Cell Games or face outright annihilation. In the Cell Games, however, is when he starts to get more overconfident and the reason he loses in the end ironically enough, is that his plan to push all Gohan's Berserk Buttons in order to make him a worthy challenge ends up workingfar too well — which, btw, was essentially Goku's plan.
King Piccolo, Cell's predecessor, counts as well. He was truly the originalMagnificent Bastard of the entire series. His first course of action upon being reborn is to send out his henchmen to assassinate every great martial artist in order to prevent anyone from using the Mafuba technique against him ever again. And when he beats Goku down the first time they met, he checks for a pulse before assuming he's dead. Too bad for him that Goku's heart started again after he left, for some reason. Also, he was also Genre Savvy enough to realize the heroes would most likely attempt to stop him with the dragonballs either before or after he got the wish, so at first, he swallowed them. Then he threw them back up once there was sure there was no-one else around left to challenge him, and to finish it off, he killed Chiaotzu when he attempted to give his own wish and interfere with Piccolo's before he could finish, and after having his wish granted, he then proceeded to one-hit-kill Shenron with his breath blast just to ensure that none of the heroes ever attempt to use the Dragonballs to defeat him.
While Vegeta was more a Smug Snake in his debut saga, he did show shades of this that made viewers appreciate him. Notably when he told Nappa to stop fighting the good guys and wait three hours for Goku to arrive because he wanted to break Goku's spirits by crushing his son and remaining friends in front of him once he got there, when he avoided Goku's spirit bomb and Krillin's disc attack meant to cut off his tail while in Oozaru form, and when he immediately realized his false moon would still be in effect the moment he saw Gohan's tail had grown back, prompting him to attempt to remove it. In the Namek saga, however, he ascended to full Magnificent Bastardry. He successfully hides his true power from Frieza and his men so that not even their scouters detect it, revealing his secret of doing this to the unsuspecting Cui before killing him. He outmaneuvers Dodoria and kills him only after being told a secret about the Saiyans' destruction. Then he implements his strategy for obtaining the Dragon Balls that will allow him to wish for eternal life: he figures he'll take just one Dragon Ball from a Namekian village and hide it underwater, then lie in wait for Frieza to gather the remaining balls. And not only is this exactly what he does, but he ends up acquiring five balls from Frieza's ship when he's taken there after losing to Zarbon in order to have his health restored (Frieza had hoped he'd tell him where his hidden Dragon Ball was), meaning he took them right from under Frieza' nose! He takes the last ball from Krillin after he had made full use of a Saiyan's power growing stronger after a previous defeat by killing Zarbon. The only reason his plan falls apart is because Gohan finds the Dragon Ball hidden underwater using a Dragon Ball locator. Even after this failure and being forced into an Enemy Mine with the good guys, Vegeta continues to employ cunning plans and come dangerously close to having his way. He lost this magnificence after his first revival due to his characterization being altered significantly to being a Hot-Blooded, foul tempered Anti-Hero, but damn if he wasn't impressive as a bad guy.
Where's Super Buu on this list? He was the most Dangerously Genre Savvy villain in the history of the series and he was only person in the history of the series that was able to Out GambitPiccolo of all people by wiping out all of humanity in only a few minutes when Piccolo was expecting him to take hours to do it, so that Goten and Trunks got extra time to train, and on top of that, never even leaving Kami's lookout while doing it. He then masterfully pulled off a Xanatos Speed Chess, when he noticed Gohan's growing power, and so he fought against Super Saiyan 3 Gotenks and tested the limits of his strength and his weaknesses (e.g. fusion limit). After briefly fighting Gohan and finding himself overwhelmed, he goes through an intentional Super Power Meltdown, knowing he will regenerate and buys time (and getting Goten and Trunks to recuperate, to fuse again). When he returns he goads Goten and Trunks into fusing again at full power and absorbs Gotenks and Piccolo into his being, deciding 30 minutes is more than enough to handle Gohan, and he was right in that regard. Goku then arrives and the fusion breaks down. Goku says Gohan alone is strong enough to defeat Buu, but then Buu reveals that he planned for this eventuality as well, and had a piece of himself ready to absorb Gohan the whole time, who he goaded into standing still until it was too late. He was also the only villain that did not succumb to Bond Villain Stupidity, which is very atypical for this series. For example, his reaction when Goku attempts to fuse with Gohan?
Although he never expected Vegeta to come back and his overconfidence gotten him a curb-stomp battle, with him being stomped on. Then again, he was able to use Vegito's own arrogance against him and absorb him too. Except that's what Vegito wanted to happen all along...
Goes back to magnificence when Vegetto defuses inside his body, which is a huge hitch in his plan. Vegeta and Goku were shocked by this; Buu wasn't.
Then again, he actually expected to absorb Vegito into himself. He was probably too angry to notice that they couldn't fuse until Goku mentioned it to Vegeta.
Also, he did try to stop Goku and Vegeta from fusing, so he wasn't exactly overconfident, and one can hardly blame him for not expecting someone he personally killed to randomly come back from the dead the very same day. Which is exactly what happened.
Kycillia Zabi from Mobile Suit Gundam, as evidenced by her lengthy and carefully calculated campaign to seize control from her older brother Gihren, as well as her skill as a battlefield commander. Various spin offs, like The Plot To Assassinate Gihren and Mobile Suit Gundam The Origin have expounded on her abilities as both a military leader and a behind the scenes manipulator, making her an excellent fit.
Not to be outdone, Zeta Gundam featured the deviously intelligent Paptimus Scirocco, who quietly manipulated his way from common lacky to becoming the head of the Titans, killing off everyone else who got in his way with a flair and style that just made it hard not to root for the guy as a villain.
Gundam ZZ has the Axis Zeon leader Haman Khan. A ruthless Lady of War and Woman in Black who manipulates and outsmarts almost everyone in Zeta, fights with honor in both series, and is so damn stylish at the same time. It rather telling that the one person that Paptimus Scirocco is cautious of (and has a healthy amount of respect for) is her.
Next, from Gundam SEED, we have Rau le Creuset, a man so intelligent and erudite he managed to mask his ever encroaching insanity and the fact that he is a clone from all of those around him. Out of all of the Gundam villains, it is quite possible that he is the only one who came closest to his goal, eradicating all of humanity.
Saralegui from Kyo Kara Maoh. In one move, he made sure that Yuuri's crew all trusted him and wiped out Large Shimaron's army by by having his own servant shoot him in the chest with an arrow, making it appear as if the arrow was aimed for Yuuri and that he had thrown himself in the way to protect Yuuri, causing Yuuri to go into Maoh mode and destroy all of Saralegui's enemies for him. He then followed that up by hypnotizing Yuuri into wiping out Large Shimaron's navy for him. Remarkably, he still managed to finish up the series with Yuuri trusting him completely until the very end.
Murata also was pretty sneaky, carrying out a 4000 year plan with Shinou in order to destroy the Originators by trapping them inside Shinou, and in turn trapping Shinou inside Yuuri to get Yuuri to destroy them both. He isn't the Great Wise Man for nothing.
Neon Genesis Evangelion has Gendo Ikari, the leader of the NERV organization. While far from his only ploy, the greatest reason he is on this page is for his involvement in the Human Instrumentality Project, even though he wasn't the one in charge. He was enough of a key factor to be considered the one most responsible for it, and he even had his own motive for manipulating its execution: to be reunited with his dead wife Yui.
Crocodile from One Piece. This guy manipulated an entire kingdom into a civil war between the king and his people while still presenting himself as a hero to the country. His entire slogan for his plan was, "The love for this kingdom will destroy it." He also added even more insult to the heroes about telling them about a bomb that would blow up the town square that was nearly impossible to stop because he had a backup in case his lackeys failed to set off the bomb. His plan was nearly flawless and would had succeeded if it was not for certain events (mainly The Hero having an enormous ammount of Plot Armor).
In a side-story that took place after his defeat, Crocodile took over his jail block and, when given a perfect chance to escape, chose to light up a cigar and stay put. He would later agree to an Enemy Mine to break out of The Alcatraz that is Impel Down solely for the chance to kill an old enemy (who, incidentally, everyone else wanted to help save).
His succesor in the Shichibukai, Blackbeard, is perhaps even moreso. The current part of his Gambit Roulette slash Batman Gambit resulted in the biggest battle/war in the history of it's world, and manipulated all sides involved effortlessly, although he admitted the plan had gone through some snags, but he still got exactly what he wanted from it: Whitebeard's extremly powerful Devil's Fruit, and 4 of the strongest prisoners of Level Six of Impel Down, which holds the worst criminals in history + the Head Jailer, a man equal to the Badass Warden. And he got away scot free, and because of the WG's pride, won't even be hunted down by them. All for his plan to become Pirate King.
Vice Admiral Jonathan of the G-8 "Navarone" facility is a rare semi-heroic example. The Straw Hat pirates just happen to fall directly into the impenetrable fortress at the same time that an inspector with an ulterior motive to have the place shut down pulls in. Rather than trying to deny the event, he takes time and makes observations about the crew, even when they show in front of his very face, turning their quirks to support a morale boost of the base's personnel and discredit the obstructive inspector. It's important to remember that his primary goal is to maintain the Marines' support of the facility, not the capture of the pirate crew, and even when things don't follow his voiced plan, he still comes out ahead.
Trafalgar Law is getting dangerously close to this after the Time Skip. Not only did he become one of the Shichibukai in order to get in close on Caesar Clown in order to stop his production of the SAD, a chemical crucial in the production of artificial devil fruits, but he also used this attempting to press Doflamingo into quitting the Shichibukai. He is also Genre Savvy enough to befriend the main protagonist, forming an alliance with him to take down the Yonkou Kaidou (who wanted the SAD chemical). And last, but not least: he tricked Caesar Clown into stabbing what Clown thought was Smoker's heart, while it in reality was the heart of his own second in command, Monet seconds before she would have released an attack that would have killed everyone except for Clown, which he would have been perfectly fine with. It Makes Sense in Context.
Buggy definitely also qualifies. Sure, he's not overly powerful, but he made it across The Grand Line just fine prior to Impel Down; once he got captured, he managed to conceal his Devil Fruit abilities while getting locked up in a supermax prison and thus avoided receiving Seastone restraints (and also managed to sneak in powerful explosives), used carefully worded lies and half-truths to talk a bunch of incredibly powerful and dangerous convicts into working for him, thereby gaining one of the strongest crews in the series, and managed to talk his way into a cushy position with the Shichibukai, ALL while operating under the guise of Obfuscating Stupidity. He's essentially John Constantine in the form of a pirate.
Manning from Orguss 02 is a perfect example of the trope. Perfect quote, when he's on a plane with two others that's under attack by an enemy Giant Robot:
Manning: "When I give you the signal I want you to push that button. That's not so hard."
Lean: "That's the hatch release. If I open the hatch, then what?"
Manning: "I'll escape in the Decimator."
Lean: "You mean the only person who's going to get out of this alive is you?"
Everything Kyouya did had a purpose that would benefit him in the long run (with one or two notable exceptions). He even used the Host Club profit to buy out his father's company unbeknownst to his dad, who thought of him as a loser because of the Club itself. Character Development later turns him into a Guile Hero.
Benibara and the Zuka Club are also contenders, having seen right through Haruhi's masquerade and also matching the Host Club in style, charisma, and persuasiveness.
Tamaki and the twins, Hikaru and Kaoru, get their moments as this too.
Ryoko Asakura of Haruhi Suzumiya fame has some qualifications down. Not only is she intelligent, but her charismatic and cheerful personality makes it so easy for one to lower their guard around her. She had Kyon and the audience fooled twice. Even though we should know better by the second time, she has us fooled anyway. Haruhi Suzumiya herself displays tendencies of this on occasion. She's at least got the ruthless, bold and charismatic part down.
Akio Ohtori from Revolutionary Girl Utena. He seduces multiple women including Utena, his sister Anthy, and his fiancee Kanae's mother as well as some guys Touga. He also: rigs the entire series of duels; creates a false timeline; convinces his own sister to stab Utena; and runs a private school in his spare time. And he gets away with all of that. ( Well, almost all. Anthy does shake off his mind control in the end and leaves him to find Utena.
Lord Laertes Van Di Montague from Romeo X Juliet, who pretty much rose from the slums after the death of his prostitute mother, infiltrated himself in the Montague clan as a kid, killed its leader when he was of age, slaughtered the rival clan of the Capulets both to gain power and as revenge for his destitute origins, and ruled Neo Verona with a hand of steel for almost 15 years. And that's just the beginning...
Kunzite from the first Sailor Moon anime. After over a season of Monsters Of The Week, most of the Shitennou repeatedly showing themselves to be incompetent, and Usagi continuing to win and even gain ground against the Dark Kingdom, it was a breath of fresh air to see Beryl's Dragon set clever traps, catch the entire team and almost finish them off (and only fail because of a scout he didn't know about), tear through Usagi's obvious Out-Gambitted ploy like it was made of wet paper, and finally go down fighting against Sailor Moon instead of getting the You Have Failed Me treatment. Even if he's not as awesome as some of the examples on this page and went through a five episode period of Badass Decay, the series could have used more like him.
Sailor Galaxia. Her super effective manipulations of all of her soldiers in the manga (and Queen Nehelenia, in the anime) as well as her sheer power puts her squarely here in this trope.
Xellos for The Slayers fits this bill quite nicely, even moreso in the original novels.
Medusa the Witch in Soul Eater. Manipulates her daughter... son... child into becoming a Dark Magical Child... but expolits Heel-Face Turnso that "s/he" would be The Mole instead. Blackmails other witches, like Eruka, into working for her by planting parts of her body in them that explode whenever she wills it. Matches the best Technician and Death Scythe in Shibusen in battle, resurrects the monster, gives The Corruption to the main heroine/hero duo, comes Back from the Dead by stealing the body of a little girl with the promise of returning it later (a promise she actually keeps but only when she finds a better body, as mentioned below) but still fully using said little girl's body as an advantage so no one can attack her, drives the best tech crazy, frames him for murder, drives out a good witch who wanted to defect, and convinces Shibusen to let her lead them in an assault against her Rival Older Sister.
In short: the only time Medusa lost, it was because she won.
Askeladd Olafson from Vinland Saga has pulled off damn near every gambit there is, kicked the dog, and kicked ass all with style. It's very easy to forget how much of a bastard he can be.
There is actually quite a suprising number of Magnificent Bastards for a manga about blood thirsty vikings.
Yu-Gi-Oh! 5Ds brings us Rex Goodwin; a very different villain given the genre. For all of the first season, he operates behinds behind the scenes, manipulating the Five Signers in order to force them to reveal themselves. For example, in order to get Yusei Fudo to participate in his tournament, he kidnaps his friends and threatens him with their deaths. Yeah. And the kicker; it's revealed that his reasons for this were inherently noble, and he has received no comeuppance for his actions. And throughout all of this, he has maintained a calm, friendly demeanor.
And then it's revealed that he used both the good guys and the bad guys for not so noble purposes, which makes him even more magnificent and even more of a bastard!
Pegasus from the original series also displayed much magnificence in his bastardry.
Bakura from the original series is perhaps an even bigger example. In his debut appearance, he's shown to be the Phaoroh's equal in being a master of all games and he manipulates all events to fit in with his "game." Afterwards, he begins a Gambit Roulette that lasts for the remainder of the series and almost brings Zorc Necrophedes, the Dark One into the living world. Not to mention that he's gleefullydeliciously and charismatically evil the whole way through.
Dartz had 10,000 years to complete his master plan, and it shows. He's set everything up so that no matter whether he and his minions win or lose, he still wins. He is the richest and most powerful man in the world owning a tiny piece of every company on Earth, and has enough capital to buy out Kaiba-Corp for no other reason than to provoke Kaiba. He has supernatural powers that outshine anything Yami Yugi has in his arsenal (The Power of Friendship excluded, naturally), has assembled the most broken deck in the series, and survived monster armies, Egyptian Gods and the loss of his own soul before he was defeated.
Sakyou from YuYu Hakusho. Even before his main role in the Dark Tournament arc, he effortlessly used Yusuke's team to cause the downfall of one of his rivals.
And later, we have the only living being able to Out Gambit Kuramaand get away with it: King Yomi. Not only he did that, but he forced Kurama to work with and for him! Fucking awesome.
There's also Shinobu Sensui, who expertly manipulated disadvantaged superpowered youths into heinous acts in an attempt to stall the good guys, forced Kurama into a situation where he would have to kill a young child in order to proceed, tricked Makihara/Gourmet into eating Elder Toguro, who took control of him and killed him, and kidnapped Kuwabara so that Gourmet/Toguro could eat him and absorb his newfound dimension cutting powers in order to destroy a powerful barrier. Later, after killing Yusuke, Sensui manipulates Kuwabara into cutting down the Kekkai barrier, which is the only thing preventing not only Sensui's plan, but also preventing Kurama and Hiei from crossing over to try and exact revenge. Total asshole? Indeed. Absolutely stylish in all of these actions? You bet your ass.
Suzaku and Younger Toguro also qualify. The former for being the first villain to really get to Yusuke on a personal level, and the latter for being the true puppet master of the Dark Tournament, Out Gambitting even Sakyou!
Although she is one of the good guys, Haruna Saotomeherself is this in regards to pactios, or anything involving magic. Ships everyone with Negi, DRAGS him to a Comiket event, and makes plans to conquer the entire Magic World.
Kurt Gödel also turns out to be one, manipulating Negi in a most magnificient and still irritating style even when he is about to be killed by him.
Dr. GraceO'Connor from Macross Frontier is slowly revealed to be a shining example of this trope. For most of the first half of the series, we are only given very subtle hints at her role in the grand scheme of things. Even the first time we actually see her working towards her goals, it's with a disguise so well done that fans were arguing if it even was her. Even the choice voice actor playing the role was seemingly meant to mislead. It's only around halfway through when she singlehandedly sets up the destruction of the planet Gallia IV where her ward, Sheryl is scheduled to perform, in the hopes of killing the latter, both as a means to win public support for the oncoming war with the Vajra, and at the same time destroying the only major piece of evidence that would link her to everything. It's also revealed at this point that she's a Cyborg with the ability to transplant her consciousness over multiple bodies. Which is why it was okay for her to personally detonate the bomb that took out the planet. Later on we learn that she was the one behind Sheryl's rise to fame, giving her the V-Type infection that had the capability of summoning the Vajra to attack whenever she sang, as revenge against the latter's grandmother, who was her former professor. The act of having Sheryl die on Gallia IV was simply due to her not living up to Grace's expectations, as well as making her revenge even sweeter; Grace had also discovered Ranka Lee, the daughter of another of her former colleagues who had better potential than Sheryl. All the while she had put Ranka's long lost brother Brera under her control via neural implants and was using him to control her. Even when Ranka rebels and flees from her duties, it's because Grace allowed it and was using her brother to manipulate her into finding the Vajra homeworld and her target, the Vajra Queen. And the reason for all this, so that she could hijack the Vajra Queen once she had learned how Ranka was able to communicate with them, and use the Vajra to take out any opposing fleets. Once this was done, she'd used the Vajra's fold communication network as a way to implement a galaxy wide neural network with her at the top controlling everyone. And all this was simply a way at getting back at her old mentor and colleague who were pretty much against the idea of such a network, for obvious reasons. And she had already succeeded somewhat by having the entire Macross Galaxy fleet under her control. Sure there were the other voices that she consulted with, but in the end, it was clear that it was her that was in control.
Legend of Galactic Heroes has quite a few, but one that really stands out is Adrian Rubinsky, who manipulates both sides of a massive intergalactic war to increase his own profit, and eventually even outsmarts and kills his own son, who had been studying from him too well and was looking to replace him.
Zolf J. Kimbley walks the fine line between despicable and admirable. Despite his psychopathic tendencies, he has a strong (if alien) moral and warrior code that he follows; one that he is aware of being at odds with society (which is why he takes great lengths to mask it). His Crowning Moment Of Awesome for this trope was when, in the manga, he came back from a disembodied spirit state to help Ed destroy Pride...and that was just because he thought Pride was being a hypocrite. He had tendencies toward this was during the Ishbalan massacre. Even though he delighted in the genocide, he was one of the very few soldiers present willing to acknowledge the full weight of his actions and remember those he cut down while others chose to look away.
"Do not look away from each new death. Look straight ahead, and never forget them. Because they certainly won't."
The Father of the Homunculi. He founded the country of Amestris to perform a ritual, hundreds of years later, in the window of a few minutes. When everyone brought the fight to his doorstep, he abused the Toll required of Human Transportation to teleport all of the sacrifices he needed straight to him. When he was short, he forced someone to transmute. When Hohenheim tried to destroy his container, he revealed that he had evolved beyond the need for it. When Greed tried to usurp him, he revealed that he had been standing in the wrong spot, since he knew Greed would try that.
Amusingly, Hayate the Combat Butler has a character who straddles the line between this and Guile Hero. Miki Hanabishi is known for her plots to make trouble for Hinagiku, in fact it's clearly stated in her profile that she enjoys it, but generally seems to be using such tactics to push Hina to the forefront of the competition for Hayate'saffection. While at the same time pursuing Hinagiku with her own romantic interest
A possible example is Mikado Sanzennin, Nagi's grandfather. A pretty much fearless Tsundere like Nagi is terrified of him, and with good reason.
Durarara!! has Orihara Izaya. Everything that happens in Ikebukuro is a result of his game of Xanatos Speed Chess. Except in book four, but he makes up for it in five and six because he felt left out.
Even more of a worthy choice is Hannah. She OutGambitted everyone in the show by having Alois take over Ciel's body and then she took Ciel's soul. Beating both Claude and Sebastian to the punch. And all of this coming from a softspoken, one-eyed Meido
Souichi of Challengers and The Tyrant Falls in Love is a relatively down-to-earth version of this. When a professor attempts to rape him, Souichi attempts to murder the guy. Morinaga stops him, but Souichi still manages to stab the guy deep in the ass with a pair of scissors. When Soichi and Morinaga witness a guy on his cellphone ignoring the pleas of a woman who has an assistive device in her heart, Soichi gets fed up when the woman collapses and snatches the phone out of the guy's hand then snaps it in half. Soichi is not a supervillain and he hasn't got the world under his thumb, but he's a damned terrifying force when his protectiveness of his brother, his sense of justice or his hatred of gays is crossed, which is often.
Vincent Nightray from Pandora Hearts also fits this title pretty well.
Xerxes Break too; he and Vincent each appear to have the upper hand on the other at points, and it's unclear who is actually the master manipulator between them.
TONS of characters are getting in on the game. Isla Yura (though there's nothing admirable about him), Duke Barma, and even Oz have had their moments. But the most jarring example: JackHolycrap.
Kanako from Star Driver, you are fighting against the Ginga Bishounen who has beaten everyone else, and you are ineveitably next on the chopping block? Why betray your call to be "professional" (splitting real life from your life in the Crux) and steal the first kiss of the Ginga Bishounen? (Without using a glass wall to make it innocent.)
Kyuubey from Puella Magi Madoka Magica. So far his plans are very cruel and have had huge consequences (like tricking young girls with deep wishes into becoming pretty much liches, then withholding info about the tremendous disadvantages of the Magical Girl job, and watching as they become witches and end up killing or being killed), but except for Madoka (the girl with the most potential) not making the contract (and once only because Homura stopped her from doing so), it has all gone just as planned. It's even better/worse when you see that his goals aren't 100% self-serving... but very akin to those of the Anti-Spiral: sacrificing some... to save everyone. And for that, he had Sayaka become a witch, then Kyoko join her in death... and thus, he left Madoka and Homura in such a position that if Madoka doesn't become a Puella Magi, the universe will die.
And even then, he doesn't exactly 'lose.' Madoka recreates the world and eliminates all witches. So instead Puellae Magi fight demons, and harvest energy from them. It's not as efficient a method of harvesting energy, but it still allows Kyuubey to accomplish his mission, just in a somewhat more modest way.
Kenneth Yamaoka from Eagle: The Making Of An Asian American President.
Rurouni Kenshin's Shishio Makoto came up with the plan to burn Kyoto right to the ground as a DISTRACTION while he and his minions sailed a warship into Tokyo and let sheer panic rip the government apart. This is just his biggest, most expensive example though. He practically lives for this trope.
The main point of Iason Mink's character in Ai no Kusabi is that he is both magnificent...and a complete and utter bastard being the most manipulative person in his world. Only his high status in society lets him get away with it.
Kokujo, of Duel Masters, uses his phenomenal skills in psychological warfare to completely destroy the hero in their first duel. The dub furthers his status by having him shamelessly call himself "an evil genius."
Toua Tokuchi, the protagonist of One Outs, definitely qualifies.
Well-Intentioned Extremist Choji Suitengu of Speed Grapher, a sophisticated businessman who uses his wealth and power in his agenda to eliminate greed and power. Oh, and he smokes rolled up dollar bills.
Knight Templar Lieutenant Colonel Dewey Novak of Eureka Seven is a military commander and aspiring dictator who knows all there is to know about charisma, sophistication, power, influence, and exploitation. And genocide, too.
The latest BakuganBig Bad Mag Mel. The guy managed to effortlessly trick the heroes into giving him the power to free himself from his prisonbefore they even know he existed. He proves to be a Manipulative Bastard and Chess Master so cunning that he's always several steps ahead of the group and even the one time thus far he's lost, he still got half of what he wanted and the Brawlers find out while they were fighting his forces on one of their ally's homeworlds, Mag Mel had utterly demolished Bakugan Interspace with another attack that cripples the transporters so no one can get out except his minions, who are free to get in and out at will. While he's not exactly charming, he realized this and made (literally) his Co-Dragons extremely charismatic and planted them in Bakugan Interspace to raise followers and generally cause chaos.
There was also Yukio Oikawa from Digimon Adventure 02. The guy was pretty much behind everything that happened in the series, and he started it all with just a simple e-mail he sent to Ken Ichijouji, a young boy wretched with guilt over his brother's death that he blamed himself for, which tells him to use the digivice he found some time ago to travel into another world. Little Ken does so and ends up in the Dark Ocean, a world of darkness and negativity which corrupts Ken into the evil Digimon Emperor. Now with Ken as his unknowing pawn, he uses him to conquer the Digital World and set up Control Spires, obelisk towers of darkness used to weaken the Digital World's defences and, in the long term, the border between the Digital World and the Real World. However, when the Digidestined defeats Ken and cleans the Digital World of the spires, Oikawa sends his agents Arukenimon and Mummymon to kill them by transforming the spires into monsters, and to destroy the Destiny Stones in order to hasten the weakening of the border. With enough Destiny Stones destroyed, the border becomes so weak that Digimon invade the Real World in thousends, and with that as a convenient diversion, Oikawa moves on to his next step. He and his minions recruits some lonely kids with promises of power and talents and then kidnaps Ken, copies the Dark Spore that was planted inside him, and transplants the copies inside the children. With time, those copies would grow into something so powerful that it would give Oikawa the final crack on the border he needed to enter the Digital World and claim it as his own. A simple goal which required complicated tactics and difficult planning to reach, and yet Oikawa pulled it all off like it was no problem at all. But then it's revealed that he was just a pawn of Myotismon all along, and that Myotismon is the true Chess Master of Digimon Adventure 02.
Devimon and Myotismon from the original Digimon Adventure could be the first ever contenders for this trope.
The franchise's greatest example would be Millenniummon, since unlike all the others he ultimately achieved what it wanted to become Ryo's Partner even though he would have also liked to start conquering the Multi Verse immediately (note that he can wait for it anyway). His actions led to nearly everything that went wrong with Digimon Adventure and Digimon Adventure 02 (including those of the ones mentioned above), but because he managed to remain undetected and completely out of reach he became The Unfought. He also succeeded in creating himself without being noticed by an omniscient being. Details can be found in the synopsis page for the series.
Legato Bluesummers from the anime. An utterly terrifying, nihilistic, relentless agent of death with the ability to mentally control any villager--man, woman, or child—to their deaths. His first appearance absolutely terrifies Vash, whom he makes his mission to completely break. And by forcing Vash to kill him, as far as he knows, he wins.
Or the manga for that matter. And in that version, he actually spent most of it crippled and still managed to remain nightmare-inducing for its entire run.
Yuto Kigai and Seishiro Sakurazuka from X1999. Yuto is polite, softspoken, a little snarky, very caring towards Satsuki and yet is able to carry out Kanoe's instructions flawlessly without even getting his suit dirty. Seishirou is a charismatic Serial Killer with a charming smile, a Star-Crossed Lovers bond with Subaru Sumeragi, very cruel and very stylish puppy-kicking acts under his belt, and in the end he manages to play one Hell of a Thanatos Gambit to die exactly in the way he wanted to, also ensuring that his killer will be the only person he ever sort-of cared for, Subaru... who will end up as the next Sakurazukamori as well..
Masako Natsume from Mawaru-Penguindrum showed quite the flair for this. Her method of erasing people's memories is a little... odd, but the rest of her actions are very effective. Kidnapping a boy to blackmail his brother and friend/prospect girlfriend? Not good. Kidnapping a boy to get the attention of his brother, staging a whole chase so said brother will remember her from his past, and then letting the kidnapped guy go... but not before giving his rescuer a Forceful Kiss, which was her intention all along? Fucking awesome.
Sanetoshi Watase is actually theMagnificent Bastard here. In his quest to regain contact with his lost "soulmate" and then bring The End of the World as We Know It, he has managed to stylishly appear to Himari in a dream, give her a new Penguin Hat, and almost get away with giving her a kiss. Later he brings Himari Back from the Dead with a mysterious serum, managing to rope her protector/brother/possible love interest Kanba into a Deal with the Devil to keep her alive. And later it's revealed that some time ago he actually forced Masako into the same Deal with the Devil so she could keep her young brother Mario alive as well. Thus, he has almost completely outgambitted both Kanba and Masako to different degrees, all while looking fabulous in that coat and pink hair of his, and specially in now hospital-confined Himari's eyes. Hmmmm!
The Major from Hellsing starts a war that levels London, manipulates all of his enemies into doing exactly what he wants them to do when he wants them to do it, and he gives one HELL of a speech. He seems to conduct everything like the conductor of a symphony, which is even lampshaded at one point. Oh, and he defeated Alucard.
Meowth meets his match when he goes up against Dr. Colress in the "Episode N" arc of the same series, who was able to play off of his overconfidence to dupe him into becoming his test subject to use against Team Rocket. Unlike the rest of Team Plasma who seek to control Pokemon for World Domination, Colress is in it purely For Science!. He clearly has no true respect for Team Plasma's leader Ghetsis (he does not speak to him with the same reverance as his grunts do), he's constantly thinking ahead of anyone else, and was always advancing his technology so that he could control the minds and hearts of Pokemon, even legendary ones like Reshiram. And he did all this in hisownstyle. Even in the end, the guy doesn't let crushing failure (and going to jail) get him down: he just vows to move on to a new approach!
Giovanni, Team Rocket's boss, has always been this. Particularly demonstrated in Mewtwo Returns and the Operation Tempest two-parter of Best Wishes, where he takes a direct role and is just barely defeated both times.
Michio Yuki from MW. He kidnaps his victims in order to extract money from the corrupt politicians who covered up the titular chemical warfare that took away his conscience. He even impersonates the women he killed as part of his plan.
MiyoTakano from Higurashi no Naku Koro ni certainly counts. She masterminded the events of the first six arcs, and loves frightening people with tales of Hinamizawa's past. She's a Well-Intentioned Extremist who goes so far as to help cause the Great Hinamizawa Disaster just for the sake of proving her grandfather's research, and the plans she makes to do so are magnificent indeed. Definitely a Magnificent Bitch. Also manages to be COMPLETELY EVIL (but mostly because of what the orphanage leader, Nomura, and Tokyo did to her).
Interestingly, Takano's magnificence is heavily influenced by a Bigger Bad and fellow Magnificent Bitch, her employer, Nomura. She demonstrated a plan to close up a company by tricking Takano into helping her and manipulating everything in order to cause the Great Hinamizawa Disaster, and nobody even seemed to notice that she was behind it all (which makes her a Karma Houdini as well). Another perfect example. Helps that she has a great evil voice provided by Rie Tanaka..
Similarly, Umineko no Naku Koro ni gives us Beatrice, an Anti-Villainwith standards who, as a Game Master, often clashes with Battler and uses magic to elegantly commit a series of bizarre murders on Rokkenjima. She's truly impressed by Battler's performance, and often looks for ways to make him surrender as best as possible. Oh, and she's also a Laughably EvilLarge Ham.
Bernkastel counts as well. Using Ange, Erika, and most other people as pawns for her plans, and planning to keep Beatrice in the game and torture her for all eternity? She definitely deserves a praise for those.
Lambdadelta. Her plan is to "trap" Bernkastel by making the battle between Battler and Beatrice last for eternity.
Higanbana of her self-titled series counts as well. Offering Marie a chance to become Mesomeso and acting as a villain against heroic characters or an Anti-Hero against villainous characters is definitely saying something.
Perhaps the most impressive and villainous character in Mon Colle Knights happens to be Redda, the Big Bad and final villain. He has a deviously cruel sense of chessmastery and mastery of manipulation, is Bishounen in appearance (especially behind that scary mask of his), and shows a nice planstarting with the part where he uses Rockna as bait to lure Mondo and all his monster friends to him, forcing him to give up all of his collected Monster Items so far and handing over to him a fake Rockna that was actually a rat in disguise. Then he summons Dread Dragon and traps Rockna within its neck, and tells Mondo that he can either destroy it and Rockna with it, or get killed himself while trying to save her without harming Dread Dragon, and orders Dread Dragon to create a wormhole that sucks up all of Mondo's monster friends. And, even when Gabriolis shows up and helps him save her so the two can fuse with him to destroy Dread Dragon, this still provides enough of a distraction so Redda can get the last Monster Item, and he succeeds in collecting it so he can finally summon Oroboros to destroy everything and create in their place a world made of nothingness, which was his ultimate goal all along. And if that's not enough, since Oroboros needs a new body in order to be resurrected, Redda revives Dread Dragon and fuses Oroboros with it to create Doomsday Dragon. Even the Laughably EvilTerrible Trio of Villains Out Shopping fear him.
Altena from Noir plays the Mama Bear role for the young saplings. However, she intentionally manipulates both the Sodats and the three saplings (Kirika, Chloe and Mireille), in order to achieve her master plan—which is to recreate the bloody history of the Sodats. She's completely dedicated and willing to die for her goal. And in the end, she does.
Naraku from Inuyasha is definitely one, if you can look past his For the Evulz and Villain Ball tendencies, especially during the Mt. Hakurei Arc, in that he manipulated a priest and a powerful group of super powered bandits into becoming his Quirky Mini Boss Squad with a few words to earn their loyalties.
Keima from The World God Only Knows can be argued to be one when he is in "God of Conquest" Mode. Even when certain events happen that confuse other characters, he simply interprets them as "flags/events" and proceeds as planned. Even for something as inconsequential as Shiori quietly yelling at him for being a jerk.
ShogoMakishima from Psycho-Pass is Wicked Cultured and highly knowledgeable in literature, music, theater and ass-kicking (he at first seems like a Non-Action Big Bad, but turns out to be a Blood Knight who is simply bored of most fights because almost no one is good enough to land a hit on him). He desires to bring down the Sibyl System that controls the futuristic Dystopia he lives in, at any cost. He also enjoys getting people to submit to their worst impulses and then disposes of them once they've lost his interest. Despite being villainous for that last part, he does care for people in his own twisted way....he believes the Sibyl System has regressed humanity by suppressing humanity's darker instincts along with their freedom of expression and ability to make their own choices. Makishima is also a master of Xanatos Speed Chess, the Indy Ploy, making allusions to classic literature (especially Dystopian literature) and making TheReasonYouSuckSpeeches to anyone. To top that off, he is an Übermensch who is literally unable to be judged by the slave morality of his world (the Sibyl System), similar to how Nietzsche himself described the Übermensch. He also becomes a Hero Killer as well, both in that the protagonists take extra caution when dealing with him and the literal sense.
Kazutaka Muriaki from Yami no Matsuei - where should I start? He's handsome, rich, works as a famous cardiac surgeon, wears mostly white clothes and is seen as an "angel" by most people. He's also a sadistic murderer, rapist and manipulative bastard. Basically, if something bad happens, you can be almost certain he had his hand in it. Did i mention that his main "goal" in "life" is to bring his dead brother back to life using the body of one of the main characters...just so he could kill his brother by himself?. Oh, and he loves porcelain dolls.
Attack on Titan gives us Erwin Smith, the Commander of the Survey Corps. Drawing partial inspiration from the tropenamer, Erwin is a handsome and charismatic leader, noted to always lead from the front and hailed as a strategic genius for greatly improving the survival odds of the Red Shirt Army he commands. He is also completely and utterly ruthless, willing to do whatever it takes for the good of humanity — described in the narrative as a man willing to cover his hands in blood and a man willing to throw away his humanity to win against monsters. Even with humanity facing utter extinction and many a Pyrrhic Victory, Erwin stays cool as a cucumber and remains unshaken in his resolve. When brought before a council and told to explain himself, he states without hesitation that his plan — which left a major city badly damaged and many dead among both the military and civilian population — was a success. The council is forced to agree with his reasoning and let him keep his command.