Russia as well. The natural result of an overgrown child with the ability to appear cute and innocent or threatening and intimidating depending on what gets them their way. He won't give choices, stating there's "no such thing as compromise in Russia". And he notes that a good thing about the German people is that they're easy to manipulate.
A rare comedic and positive variant is presented in Bakuman。. Kazuya Hiramaru is a prodigy mangaka and managed to get his very unique and comedic manga Otters 11 published very early on. Sadly, he's near-pathologically lazy, incredibly Book Dumb, and his behavior makes him somewhat of a Comedic Sociopath. note Naturally, he came as one of the top 3 in the popularity polls. His editor, Koji Yoshida, both recognizes his capabilities and figures out how to manipulate his emotions, but he only ever does so in order to ensure that he keeps on writing splendid manga for the people to enjoy. It's his job as an editor, after all.
Griffith from Berserk really likes to emotionally manipulate people for his own ends. From holding Foss's daughter hostage to foil an assassination plot, to pretending to be in love with Princess Charlotte so that he can marry her, to giving Casca the strength she needs to defend herself and thus gaining a powerful fighter, to pretending to be Guts's friend and gaining himself an even stronger fighter, to giving thousands and thousands of people, including the Crystal Dragon Jesus equivalent of the Pope, visions of a saviour defeating darkness so that half the world effectively rallies behind him, Griffith does qualify for this trope to say the least. The Godhand as a whole to a lesser extent, as they offer people demonic powers and make them give up their loved ones at their lowest point. The goal of the Godhand is just making Midland an even shittier place to live in, though.
You must admire his prophetic vision. To be able to spot a skinny, half-starved girl-child about to be raped in a field and know that she would grow up to be an amazing warrior completely devoted to him if he'd only save her is pretty impressive.
He didn't "know" that Casca would grow up to be an amazing warrior. He seems to do this with almost everyone he meets; the ones with potential rise up in the ranks, and the ones without remain grunts.
It's debatable how bad he was initially. Most effective leaders create personal connections with their subordinates to motivate them; it's also pretty obvious he felt somethingor other for Guts and Casca. That said, his seducing Charlotte, kidnapping Foss's daughter and everything post-Eclipse put him squarely in this trope. Among others.
In Bleach, none other than... Sousuke Aizen. No other Manipulative Bastard deserves more hate than him.
Also, Ichimaru Gin. Boy, does he love pulling people's emotional strings. He even manages to deceive Aizen and then attack him. He also lied to his old superior about his bankai ability.
Urahara is another example.
In Brave10, Hanzo is cunning and manipulates his opponents' and teammates' emotions alike to achieve his desired ends. And while Yukimura is generally working towards the good of those he cares about, his manipulation of the Braves as well as his enemies brings him into this territory more than once.
Code Geass: Lelouch Lamperouge isn't as bad as you might think in this department, considering his Geass, which only works once per victim, but he still has his moments. The greatest example of this comes in the second season: Rolo, Lelouch's fake little brother, was actually a teenage assassin charged with the task of keeping an eye on Lelouch in case he regained his old memories. When Lelouch found out, he continued treating Rolo kindly and orchestrated a situation where Lelouch could pretend to risk his life to save Rolo, winning his trust and bringing him over to his side. After Lelouch's real sister died, he admitted to Rolo that he was just using him, actually hated him, and had tried to kill him on several occasions. Nevertheless, without being asked or influenced by Lelouch's Geass, Rolo sacrificed himself to protect Lelouch. and There's also his evil, evil abuse of Suzaku in ep. 18 of Season 1. He'd found out from Mao that Suzaku's father hadn't killed himself, Suzaku had killed him and been carrying the guilt about it around for years. So when he, as Zero, has Suzaku trapped and wants to convince him to switch sides, he makes a Not So Different speech predicated on the fact that the Prime Minister's death was murder, not suicide — but he delivers it as if he expects this to be news to Suzaku. He doesn't reveal that he knew about it until Suzaku has melted into a little puddle of guilt and self-loathing. Lelouch, you are a terrible person.
He only had to yank the kid's chain lightly. Rolo seemed already infatuated with him, wanting to be his only family, only friend. And lo and behold, did that end up blowing on Lelouch's face. (Poor Shirley).
And he did it to Suzaku to try and guilt him to joining his side. The alternative was using his Geass, which he did not want to do.
Schneizel is even more dubious. He builds his entire reputation on manipulating characters and expertly derails Lelouch close to the end.
Later on it turns out that C. C. knew the truth about Marianne's murder and was just stringing Lelouch along so that he could grant her wish to have her code, and along with it, her immortality taken so she could finally die. Later on she regrets this, and asks Lelouch if he hates her for it. He doesn't.
Villetta Nu could be considered one for using a distraught Shirley to expose Zero's identity and causing Shirley to break down even further when she figures out that Zero is her beloved Lelouch and Villetta attempts to goad her into turning him in. And given Alternate Character Interpretation (if not carrying the Idiot Ball), she just might qualify for this for convincing Ohgi to use the circumstantial at best Geass evidence on Lelouch against him, when she more than likely knew more about Geass.
Light from Death Note. He managed to manipulate a shinigami into killing L at the cost of her own life for chrissakes. Plus getting Naomi Misora's real name out of her simply by smiling, listening to her theories and then lying through his teeth. Not to mention he manipulated the task force into believing his innocence and accepting him as their leader for years. Light really is the expert on taking people's emotional investments, patterns of thought and trust in him and twisting it all to his advantage.
To some extent, L also qualifies. His main strategy seems to be "jerk Light around until he slips up and reveals himself as Kira." He manages to convince Misa to join him in his investigation of Yotsuba by playing on her concern for Light's safety... and then in the same breath convinces Light to join him by playing on his concern for Misa's safety - which was only jeopardized due to her joining the investigation.
Demidevimon/Picodevimon of Digimon Adventure is a good example, having used deception and played on their fears to keep the Digidestined apart after they split up to look for Taichi and Agumon, as well as to prevent their crests from glowing (causing T.K./Takeru to despair, Joe/Jyou to appear unreliable, Matt/Yamato to doubt Joe's friendship, Koushiro/Izzy to trade away his curiosity, Mimi to act selfishly and deceptively, and Sora to believe she had never been loved). The only reason he ended up failing was because Taichicame back.
Cherrymon/Juraimon also manipulated Matt into turning against the other Digidestined, especially Tai.
The greatest Digimon example, however, has to be DarkKnightmon from Xros Wars, who gained multiple long-term allies by toying with their emotions.
Izaya Orihara from Durarara!!. The first time you properly see him in the anime, he spends most of the episode having a girl, that he pretended to sympathize with online, kidnapped and then orchestrating her rescue, only to hold her over the side of a building, toy with her desire (or lack thereof) to actually commit suicide, and then wander off to watch from a distance as the girl decides to jump anyway. (Luckily for her, someone else was a little more worried about her safety and saves her.) Anyone who meets him in the series is wary of him, has a number of tales to tell about how manipulative and dangerous he is to be around, or just skip the talking completely and throw vending machines in his face.
Hiruma of Eyeshield 21. Even with all of his manipulation, he's genuinely cared for his team. It wasn't much manipulation more than giving them reason to fight, pull the miracle, and win.
Marco Reiji of the Hakushuu Dinosaurs as well. He plays with the emotions of his own teammates and those of the other team to the extreme. Unlike Hiruma, who's also a Chessmaster, Marco will settle for screwing with your head.
Angel of the Oración Seis is a pretty manipulative bitch too. Especially when she summons Aries, someone Loke is very close to, to fight him.
Shigure from Fruits Basket belongs to the Obfuscating Stupidity category of manipulators, but still manages to get away with lots of mind games while remaining rather sympathetic.
Akito, from the same series, is more Manipulative Bastard than passive-aggressive, although a case could be made for both. He ( or better said, she) has sufficient status to ensure that he is obeyed, but prefers to deploy the tyranny of the weak (due to his illness) and mental/physical torture to make absolutely sure that he controls their souls. After a massive Break the Haughty, however, Akito manages to get better.
Nakago of Fushigi Yuugi is a prime example of this. One main reason: he manipulates the heroine Miaka's best friend Yui into believing she was raped and betrayed, and also plays off of her unrequited feelings for Miaka's lover Tamahome, effectively turning the two girls into archenemies. He also appears to like going out of his way just to screw with the characters' heads, even when it no longer serves a real purpose.
Future GPX Cyber Formula has both Henri Claytor and Kyoshiro Nagumo (who can be considered to be Durandal's Expy), in ZERO and SAGA respectively. Henri in particular, in which episode 5 of ZERO shows him playing mind games with Shinjyo, Gudelhian and Heinel to make them believe that Hayato is crashing other racers to get ahead.
Kirie of Girls Bravo displayed tendencies of this sort in the anime, like in the the second season when she emotionally manipulated Yukinari into cross-dressing for an event and allowed Fukuyama to practically molest Yukinari since it meant Fukuyama would pay her for it; and she didn't get punished for her actions either.
Vetti Sforza of Glass Fleet seems to prefer to use emotional manipulation to accomplish his goals. During his Start of Darkness, he seduced, if not actually raped, his foster mother in order to manipulate her into killing his foster father. Then, since she was no more use to him, he killed her. During the series itself, he exerts considerable effort to persuade Rachel, the daughter of the Pope, to marry him. Although she eventually agrees to marry him for political reasons only, Vetti goes the extra mile to get her to fall in love with him for apparently no other reason than to be able to snub her later.
Tohma, from Gravitation, is a variant. He's certainly adept at messing with people's heads and hearts, being an extra-special bastard to hapless and naive Shuichi. However, he doesn't really care about his victims' emotions... well, maybe he gets a bit of a power trip out of it. Mainly however, he's invested only in Yuki's feelings. He maintains that everything he does is to protect the novelist, but by doing so he also maintains Yuki's dependency on Tohma himself. As a result, his nastiness to Shuichi is due at least in part to jealousy.
Yuki himself is a Manipulative Bastard / The Vamp to his boyfriend in the manga, and makes no secret of the fact. At one point, he taunts Shuichi by saying that he's only nasty because that's the romantic ideal that Shuichi wants. Since the anime is less convoluted than the manga, this aspect of Yuki's personality is played down, making him a Jerk with a Heart of Gold instead.
Nagi Sanzenin's grandfather, Mikado Sanzenin, has proved himself one of these in chapter 249 of Hayate the Combat Butler. In past chapters he essentially plays with Nagi's status as a target for people after the inheritance, which is reason enough. In the latest, he forces Hayate, her butler, into deciding her lifestyle, forcing him to choose between protecting a stone which has become the symbol of the Sanzenin inheritance, or breaking it to save his former girlfriend's life. And to make it even worse, he admits to manipulating the boy's life ever since he can remember by posing as innocuous figures. The only thing redeeming about him is the fact that he genuinely loved his daughter, favors his granddaughter's maid, and taught said granddaughter how to invest.. so she's not rendered completely poverty-stricken when the inheritance gets taken away from her.
The Major in Hellsing is the ultimate manipulative bastard. He has no super powers, is weak enough to be beaten down by an old man, needs glasses, and can't shoot. How come then he is in command of a battalion of 1000 SS-vampires? He simply manipulated them and won their respect. Many of his soldiers would gladly go on suicide missions or even commit suicide for him. One can understand that many would do anything in return for eternal life, but the Major can make men who has eternal life obey him. Some have suggested that they might be brainwashed but it's stated quite clearly that these men are volunteers and are acting on their own free will.
When one of his "superiors" confronted the Major about his plans and why he had disobeyed their orders the Major provoked him and was hit. All of the present soldiers responded with pointing their guns at him for threatening their beloved leader. None of them ever questioned the Major's actions or plans.
One of the few non-SS members refused to obey the Major when he ordered a final full frontal attack on Alucard's familiars for fun, because he refused to see men's lifes wasted for nothing. The other members of Millennium quickly asked the Major is he was to be disposed of. He was.
Q-Ta from Honey Hunt has a desire to monopolize Yura in a decidedly unhealthy way, bringing to mind the worst of the controlling, abusive tendencies exhibited by Ryoki from Hot Gimmick. The difference here is a level of scale and dysfunction, as the much slicker Q-Ta (who has shades of Azusa) is much smarter about getting what he wants without having to resort to underhanded tactics. For example, the whole "I guess you like Keiichi (her manager) more than me" thing he pulled to get her to go to the hot springs and miss her curfew and Nanase's dinner was subtle emotional blackmail.
Also, Natsue Tachibana. She delights in manipulating the lives of those beneath her, starting malicious rumors and relocating workers based on their family's reputation. Multiple times she tries to separate Hatsumi and Ryoki, seeing Hatsumi as unsuitable and undeserving of her son. Natsue is presumably obsessed with controlling the people of the complex because she has almost no control in her own family (Ryoki never listens to a word she says and rebuffs her concerns with no emotion, and Shuichiro, in his rare appearances, easily undermines her at every turn).
Higurashi no Naku Koro ni: In "Saikoroshi-hen", it is revealed that that world's Rika was one of these towards all of the boys her age, which is why she's so alienated from her friends.
Fuyumi Irisu of Hyouka deceives the Classics Club into writing the script of the unfinished movie without letting them realize it. Oreki, however, figures it all out soon after.
Naraku of InuYasha loves to do this, and his creations and minions often favor it as well. Naraku's favorite tactic is to turn people with close relationships against one another - for example, the nearly series-long campaign he wages against Sango by controlling her little brother Kohaku and trying, repeatedly, to provoke her into killing Kohaku. In the finale, Kagome turns this against him by pointing out that his ability to manipulate people so effectively was proof that he still had a human heart. This ultimately leads to his defeat.
In JoJo's Bizarre Adventure, this more than anything is why Dio Brando is so dangerous. His vampiric abilities, the power of his Stand to stop time...they pale in comparison to his ability to charm and bend others to his will. Most of the enemies in Parts 3 and 6 are composed of those who have been charmed to his side, whereas another of his followers plays a major role in the plot of Part 4.
From Kekkaishi, we have Kaguro. He can look at you, and immediately know how to hurt you emotionally. He pushes all those little buttons, up to and including making sure to kill people close to his designated target to further play with them. He even psychologically dissects his own ally, Aihi, right before killing her for no reason whatsoever. Even during his battle with Yoshimori, he talked a lot, goading Yoshi on for the first part of the battle. This ends up his undoing.
Niijima Harou from Kenichi: The Mightiest Disciple is this at first. He manages to create the Shinpaku Alliance through a combination of deceit, blackmail, bribery and outright lies. Has at times exibited traits from most of of this trope's subtypes.
Kyo Kara Maoh!'s resident trickster, Murata, is a more benign version. He lets Yuri and company walk into trouble just because he likes seeing how they react, even when he knows enough to prevent the trouble in the first place. His Omniscient Morality License lets him get away with it without Wolfram or Gwendal killing him out of frustration.
In The Legendary Moonlight Sculptor the main character Weed, as a result of a tough childhood being chased by loan sharks and supporting his younger sister and grandmother, has developed an extremely cynical view towards the world, to the point that he almost flunks the elective morality section of his Korean equivalent GED test. He himself is a remarkably intelligent person, and through years of underaged working and dealing with manipulative adults, has developed a silver tongue and unrelenting drive. Now that he plays the VRMMORPG Royal Road to make money selling items, his full potential as a Manipulative Bastard has come out. He discovers and finishes high ranking quests on his own that normally take several hundreds of players. The biggest example of this is his achievement in infiltrating the orc NPC's with an illusion, to gain their trust, and then lead them in battle against a dark elf fortress, and then lead both of these factions against a lich's undead legion, in an unheard of battle involving over 2 million NPC's.
Virtually everyone in Liar Game. Particularly Yokoya, but Akiyama with alarming frequency, such as when he pretending to invent a method to determine who was 'infected' and who wasn't during the Pandemic game in order to learn everyone else's status.
The Loveless cast is full of both true Manipulative Bastards and passive-aggressives — some are both at once. This is most likely because everyone is trying to manipulate someone else, while having serious emotional vulnerabilities of their own.
Case in point: Soubi. He's constantly trying to maneuver Ritsuka into doing what Soubi wants him to do at the start of the manga. Turns out Soubi himself was badly abused and manipulated by a whole herd of people, including Ritsuka's big brother. To further complicate matters, Soubi becomes subservient to his "target," Ritsuka.
Nagi in Mai-HiME. It's his "profession", as one of the perpetrators of the HiME Carnival, to trick the girls into eliminating each other by playing with their fears. His Mai-Otome incarnation was also like this at first, but eventually transformed into a Smug Snake.
A particularly disturbing mention must be given to Yuno in Chapter 49: Yuno cuts herself with a knife after fighting Akise and covers herself in blood, and is trying to reach Yukiteru before he kills the 8th and Hinata/Mao/Kousaka. Yuno calls Yuki and tells him that her diary told her that they (his friends) were going to betray and kill him and that Akise was trying to kill her. Yuki, in the middle of a mental breakdown at the time, believes her and shoots (and assumedly kills) Hinata. Yuno, on the other line, starts laughing her butt off, while a shot of her diary reveals that, no, Yuki's friends weren't trying to betray or kill him. She just didn't want them to have him.
Katejina Loos of Victory Gundam manipulates Uso and Chronicle, just to satisfy her own vain ego of seeing both males fight for her favor. Fonse and Tassilo try to manipulate Queen Maria, to use her as a puppet, while they truly run the Zanscare Empire from behind the scenes.
Johan Liebert from Monster is directly responsible for the deaths of a fairly small number of people, he prefers to have conversations with anyone that interests him and, very politely, talk them into committing acts of mass murder or just killing themselves. In fact it's rare for Johan to leave a room without leaving someone Mind Raped to the point of temporary paralysis. He's just that evil.
He got everyone in a peaceful little town in the countryside into a state where just a little push would turn the place into a veritable warzone. He also once sent a boy looking for his mom into a red light district, telling him in the kindest voice imaginable that if no one claims him, it means no one in the world loves him. The heroes only catch up to the poor kid seconds before he was about to jump off a bridge. It's one of his most despicable acts in the series, which is saying a lot.
All the kids he talked into playing a suicidal 'game'; apparently just for the heck of it.
Michio Yuki from MW. Manipulating and blackmail the corrupt politicians involving with the titular chemical warfare into handing over the money to him; once that is done, he kills them.
Orochimaru is somewhat unusual, in that he normally doesn't target the heroes (although he is adept at Breaking Speech, and seems to teach it to those closest to him as well). Instead, he seems to specialize in finding traumatized young ninja and using his manipulative powers to turn them into his devoted followers.
What little is known about the Kazekage points to him falling under this archetype. He used his own son to gain power, killing his wife in the process, and began his campaign against Gaara's sanity. Social isolation, no contact with his siblings, and multiple assassination attempts, culminating with the one person Gaara trusted (whom the Kazekage forced to lie about hating the kid, and then commiting suicide over it), all results of the Kazekage's decisions, drove Gaara beyond the Despair Event Horizon, finally netting the Kazekage the uncaring weapon he desired. Until Gaara is defused by Naruto, and when the Kazekage is revived by Kabuto, he gets to epically call his dad on all of his shit. His dad is genuinely regretful about it, though. It's clear that he didn't want to do it, but felt that he had no other choice when it came to the well-being of Suna.
Also, Kabuto Yakushi, Orochimaru's right hand man. He has shown himself to be a very skilled manipulator. For years, he was able to convince the entire Leaf Village into believing he was a genuinely kind-hearted man with inept shinobi skill outside of medical skills (to which he made it appear he was only decent at) to make it easier in gathering information. He is also able to use his strong powers of deception to fool his targets into aiding him in several manners and rather enjoys playing mind games with his enemies, often unnerving them by pointing out their weaknesses and turning personal horrors against them.
Black Zetsu manipulated the conflict between the Uchiha and Senju clans for generations in order to revive Kaguya, even going so far as to rewrite their history to guide them down the right path.
Kurt Godel from Negima!! Every single thing that the man has done is part of a massive ploy to get Negi to do what he wants...Revenge for the unjust incarceration and near-execution of Queen Arika, who was both Negi's mother and the love of Godel's life ever since he was a teenager. Bloody, fiery revenge.
It is not uncommon at all to find a Chessmaster in this series, many of whom fall under this trope as well.
Crocodile. He managed to come within a hair's breadth of overthrowing an entire country and becoming king of it through sheer manipulation and deceit, organized over the space of three years; to emphasize how much of a task this was, the ruling royal family had centuries of trust built up with its people. The only thing that kept him from succeeding was the intervention of the Straw Hat Pirates, supreme Spanners In The Works, who the country's princess had the good fortune of befriending.
Sakazuki of the Marines, also known as Akainu. Easily the most ruthless of any Marine seen thus far, he has no conscience whatsoever when it comes to pirates; anything short of his superior's orders will not stop him from making every attempt to kill them, no matter who suffers along the way. His manipulative skills are prevalently shown during the War of the Best, when he not only manages to turn one of Whitebeard's allies against him through a few false statements, but also deliberately smashes Ace's Berserk Button to get him to attack him, resulting in Ace's death.
But nobody can fit this trope better than Donquixote Doflamingo; for starters, he's The Don of the entire New World—perhaps even the entire Grand Line—and he succeeded where Crocodile failed, overthrowing a country and taking over it thanks to a well-engineered frame-up which erased centuries of trust with the then-current royal family in a single night. But he's not just this trope verbally and emotionally—though he excels in those also—but physically as well; thanks to the powers of his Ito Ito no Mi (String-String Fruit), he can make People Puppets in every sense of the term.
Fukiko from Oniisama e..., especially to Rei, and later to Nanako, whom she manipulates Nanako to keep her crush Takehiko (the titular Oniisama) and stop her from writing letters to him.
Both Sae and Ryo from Peach Girl play with people's minds by relying on their ability to charm people into doing what they want. Ryo's manipulation/mistreatment of Sae is so bad, though, that it's enough for her to change her ways. Sort of.
Count D, in Pet Shop of Horrors, loves to watch humans dig traps for themselves, with a minimum of encouragement from him and his pets.
D finds himself Becoming the Mask, though, with his growing attachment to Leon and Chris. He becomes increasingly sympathetic towards humankind only to be badly affected when a girl he felt some responsibility for dies.
He's still a Manipulative Bastard in the sequel, though.
Doe-Doe from the manhwa Pig Bride is a very subtle seductress: She's a violent, foul-mouthed, girl-gangleader-bully of the whole school disguised as a sweet and innocent girl trying to win the heart (and money and political power) of the main character. So far it's worked, although the main's friend really dislikes her but can't put his finger on why other than the fact that she doesn't know her target's heart at all ("He must love living in such a luxurious house!" "Actually he hates this house and couldn't care less about luxury").
One person on MangaFox declared her to be worse than the Rich Bitch from He's Dedicated to Roses, who had been using the main character as her Beleaguered Assistant for years thanks to her mastery of the Wounded Gazelle Gambit. At least that girl never (personally) tied up her "maid"/romantic rival and threatened to leave her in an empty building for a weekend, but then again she wasn't a desperate golddigger either.
Meowth from Pokémon has done this several times throughout the series, but what took the cake was in Best Wishes, where he lies about being kicked out of Team Rocket, gains the trust of Ash, Iris, and Cilan, and unveils TR's most malevolent plan to date.
In Ranma ˝Fanon, Nabiki Tendo is often made into one of these. In the actual Canon some would argue that she is too hedonistic to qualify, is more of an opportunist than manipulative, since she generally takes advantage of situations for swindling, blackmail, entertainment, and revenge, rather than engineer them from scratch herself. She has been able to successfully lead (susceptible and rather predictable) targets through hoops by manipulating their emotional reactions (better at it in the anime than the manga), can quickly make up several minor backup plans, such as manipulating Ranma into producing sounds akin to attempted rape, is skilled at acting and hazard games, has virtually unflappable self-control when she feels like it, and predicted her rival's plans by tampering with his parachute in advance and then demanding victory to throw one to him as he fell.
Ranma Saotome, a Manipulative Bastard, particularly in the manga. Tricking, deceiving, manipulating and outright blackmailing others into doing what he wants (or for the fun of it) is a common thing for him. His personal style of fighting can even be reasonably said to have a firm grounding in finding ways to use distractions, ambushes, cheap shots, exploit weaknesses, and play headgames with his opponents.
And that's why his style is called "Anything Goes Martial Arts."
Wiseman from Sailor Moon uses Chibi-Usa's feelings of inadequacy and abandonment to turn her evil. He twists Prince Diamond to his purposes by preying on the prince's feelings of rejection and bitterness at the moon kingdom. And he also tries to manipulate Sailor Moon into believing that Mamoru and Chibi-Usa don't care about her and have abandoned her. Death Phantom cares little for his pawns; he manipulates them, and kills Rubeus and Saphir himself. He also humiliates Esmeraude when she comes to him asking to be the queen of Nemesis, and brings about her transformation into a dragon and, ultimately, her death.
Dr. Nii also known as Ukoku Sanzo from Saiyuki, since it turns out he's been behind everything in the manga story so far in one way or another. Gyokumen Koushu also qualifies, especially towards Kougaiji.
Kyoko from Sangatsu no Lion has made several attempts at manipulating Rei toward losses in professional shogi.
Sekai from School Days. Specifically in the manga version.
Xellos, in Slayers, is particularly adept at this, especially in the novels. Seriously, just read novels 7 and 8 to get a good idea of how thoroughly he can screw the protagonists over. You know you're good when your victims know you're up to something and still fall for it hook, line, and sinker.
Albert Maverick from Tiger & Bunny turns out to have been extensively manipulating Barnaby for years. How much so? Over half of what Barnaby remembers of his past is a complete lie. He doesn't even realize that he actually grew up in an orphanage◊ rather than under Maverick's care because of the constant memory alterations.
Seishirou in Tokyo Babylon shows to be an extremely good liar, and wholly shameless about it.
Tokyo Ghoul has several of these, manipulating events behind the scenes and trying to outplay each other to achieve their own ends.
Eto is a mastermind with grand schemes, using her brilliant mind and knowledge of human psychology to control everything around her. She uses Ghoul Supremacy as a means to create an organization to serve her goals, then establishes herself as a minor member to keep tabs on her subordinates. When she finds a useful pawn, she uses one of her many identities to approach or observe them, and then uses their emotional or mental issues to twist them to her way of thinking.
Nimura Furuta, a Double Reverse Quadruple Agent in the service of the organization V. A more hands-on manipulator, he gleefully plays whatever role is necessary to achieve his goals and has infiltrated numerous organizations over the years. During his introduction to the series, he seduces an unsuspecting woman with promises of marriage in order to lure her to a Nasty Party where she is cooked alive for his entertainment. In his primary identity, he plays the role of an incompetent subordinate and manipulates those around him for the (apparent) benefit of his superiors in V. But he also reveals that he is involved in betraying even them, giving aid to enemy organizations such as Aogiri or allowing Kaneki to obtain damning information about the leaders of the CCG. He claims this is for "personal reasons", refusing to reveal what his true motivations or goals might be.
The Tower of Druaga: The Aegis of Uruk has two of these, though Neeba is probably the closest to Magnificent Bastard status. He even tells his party members that they are going use the blue crystal rod to rebuild their dead friends hometown. Then, he kisses The Lancer, just out of the blue. She promptly melts and gets enough of a morale boost to last right up until The Reveal. How does he repay his friends after the Big Bad is dead? By shooting The Big Guy in the kneecap with an arrow. The only person he was ever honest to was his brother, whom he thinks is 100% worthless with no redeeming value.
Kaaya is also pretty Manipulative of her Five-Man Band, as well. She even lets Her literal and figurative Lancer die , in addition to playing the Protagonist much the same way that Neeba played Fatina, however, this Manipulative Bastard seems to feel genuinely sorry about it. The pair's only slip-up was that they left a perfectly good five man band and two army officers alive - albeit separated - and really, really wanting to kick their ass.
Kaaya actually is not all that great at this trope. While she had intended to use them to accomplish her goal, she was a compasionate person at heart, and quickly came to care for her companions (along with genuine feelings towards the protagonist). She also knew that she was leading them towards certain death, and this weight became heavier the longer she traveled with them. Her betrayal at the end of season one came about because she simply did not want to see her friends killed.
Sideways, from Transformers Armada. If something happens that isn't directly related to finding a Minicon, this guy's behind it.
Wolf Guy - Wolfen Crest: Haguro. Manipulates the younger Kuroda into going Columbine on half the student body out of vengeance against Inugami for his brother's death. Using weapons from his family gun cellar. The kicker? His brother died because HAGURO pulled his life-support.
Pegasus, Marik, Dark Bakura, and Dartz from Yu-Gi-Oh!.
Quite a few of the Hentai productions out there that showcase material that live adult movies couldn't get away without breaking countless laws have Manipulative Bastards of both genders as protagonists. In the cases where the protagonists are the victims, then every other character will be a Manipulative Bastard. It reaches the point where the plots focus as much on Mind Rape as they do on actual rape.
Vegeta: He's actually quite cunning when he's not letting his arrogance or rage get out of control. Particularly in the Namek Saga; he bordered on magnificence there. He went into that conflict knowing beforehand that he was hopelessly outclassed on several levels in terms of battle strength (in other words he came in with a humble perspective from the get-go), and his second most cunning moment (at the end of the Buu Saga) came just after he finally admitted to himself that Goku was the better warrior. In short, the cunning gets turned on when the arrogance gets turned off.
Cell: Particularly in his first two forms, where he's driven by a single-minded focus to become complete and is forced to use cleverness rather than strength to accomplish it. Likewise, he knows his enemies' personalities very well, so he knows that, say, letting them retreat only allows them to recoup their efforts. So whenever anyone attacks him that he can deal with, no matter how important his business is he always takes the time out to deal with them before proceeding. In his second form, he knows Vegeta's ego and drive for seeing a real battle well enough to ensure that Transformation Is a Free Action. Because Cell was made up of the cells of Vegeta and other pure blooded Saiyans such as Goku, Raditz and Nappa, he knew that Vegeta's greatest weakness is his pride and that a Saiyan would be willing to go to great lengths for good battle because they love a challenge and love to fight. Cell then uses that weakness to manipulate Vegeta by telling him that if he had the chance to reach his perfect form he would become a worthy adversary, and he claims that Vegeta would be no match for him. Vegeta, who hungers for a challenge, any chance to prove that he is the best no matter what the risk and thrives for any good fight in general, lets his ego get the best of him and steps back from battle, allowing Cell an open opportunity to absorb Android 18, and stopping Trunks from interfering. Cell proceeds to No SellEVERY attack Vegeta throws at him, kick Vegeta’s ass senseless with little effort and rub in Vegeta’s face how stupid he was to help him achieve his perfect form and become more powerful and how he should have killed him when he had the chance. While Perfect, he knows that the best way to make a hero mad is to harm his loved ones... so he does.