The Practical Incarnation from Planescape: Torment. He gets a woman who knows he's a Manipulative Bastard but is still in love with him to accompany him to her certain death so he can have a spy in the place where she'll die. He creates a holy text quite possibly wholecloth in order to get a member of a race that freed itself from slavery and despises the notion to swear fealty to him. He gets a blind archer to effectively sell himself to him. Manipulative? Oh yes. Bastard? Yes.
And, depending on how you play the game, the player character can be as well. If you're smart enough, you can actually out-manipulate the above Bastard.
Half of the cast from Metal Gear. Liquid Snake and Solidus Snake are famous for tricking the heroes. However, the award of biggest manipulative bastard needs to go the Patriots and Revolver Ocelot.
Resident Evil: Albert Wesker. In RE1, he blackmails Barry into betraying Chris and Jill by holding Barry's family hostage so that three would kill each other. In RE5, he captures Jill, turns her into his slave against her will, and forces Chris to fight against her, for the same reason as before.
EVE Online. One of the main ways to succeed at EVE Online is to become a manipulative bastard. It's not the only way, but most players are bound to go this path.
The most infamous example being Cally - aka Dentara Rast - who, after forming a corporation called the EVE Intergalactic Bank (EIB), transformed his above-board loan dispensing enterprise assisting new corporations with start-up capital and the sale of desirable tools and other in-game items (complete with loans and associated repayment schemes) into what is arguably regarded as one of, if not the, largest scams ever legally conducted in a video game. From the initial start-up capital for his own corporation (100 million ISK - EVE's in-game currency), Cally utilised various means such as verbal misdirection, inventing a friend (Peter) to whom he had "entrusted" the reins of the corporation and, at one point, even faking his own death (in the eyes of his fellow EVE players) to rake in a cool 790 billion ISK; increasing his own money almost eight thousand fold. The best part of the whole scheme? The sixteen-minute video where he admits to and brags about the entire thing.
Cally: I didn't break any rules. I didn't hack into your accounts and take the money. You gave it to me. And there's nothing you can do about it.
Ratchet & Clank: Ultimate Supreme Executive Chairman Drek deserves a mention here. He's quite good at what he does, has an impressive voice (done by Kevin Michael Richardson) and has eyes that are large, shiny and blueish with no pupils.
However, he's been killed by Hakumen, and it turns out that all along he was playing into Izanami's hands.
Hazama's partner in crime Relius Clover is a fine manipulator too; he's spent years trying to play piano with his son Carl's emotions, often for nothing more than amusement. He tricked into helping him create Ignis. In her legendary Bad Ending, he mind rapes the above Makoto into borderline catatonia when even Hazama, himself a pro, failed to do much. Recently he's been trying, with considerably less success, to play Litchi.
The Warcraft series seems to love this kind of villains. Kil'jaeden The Deceiver is probably the biggest of these, doing countless Gambit Roulettes behind the scenes and rarely, if ever lose his cool.
Every single member of the Black Dragonflight you meet are manipulative bastards in their own right, seemingly a requirement to be a black dragon, even the ones who aren't downright evil such as Sabellian aka Baron Sablemane and the supposedly purified Wrathion manipulated the player character for a great deal and only showing them their true form and purpose when they have trusted the player character enough.
Lich King Ner'zhul himself, he manipulated Kel'Thuzad, Arthas and Dar'khan Drathir, aiming at their desires (thirst for knowledge, revenge and power).
Gul'dan was the first Manipulative Bastard in the entire Warcraft franchise, even before the character of Kil'jaeden was fleshed out.
Axel from Kingdom Hearts: Chain of Memories, playing both sides in an Organization XIII internal conflict so that he could feel amused (hey, when you're a Nobody, you'll take any feeling you can get.)
Marluxia and Zexion from the same game, though the latter tends to fall into Smug Snake territory.
Maleficent definitely count too. In the first game, she had gained the loyality of Disney's most ruthlessly evil villains by promises of high power of galactic scale, something most people whouldn't ignore. She also played Riku into her hands by using some good old fashion "play on his jealousy of his best friend, 'cause he has the girl and greater powers" while playing the mother figure to him.
Master Xehanort manipulated the three protagonist of the first game so he could get a new body, get Kingdom Hearts and restart the Keyblade War. Even after the prequel's end he still succeeded with one of his goals. Not only that but even after his two halves are defeated he's going to make a return as the original. It's as though this is just another alternate plan he created in case his other halves failed. The events of all of the games but 1 is due to him, and you could say he was responsible for that game being necessary at all.
In the Fallout series you can get out from/make almost any/every situation if your Speech-skill is high enought...this depending are you good or evil. In Fallout 3 alone - when playing Good - you can negotiate/seduce a man to give up his plan to blow up a city or - as Evil character - manipulate him to double the reward if you want to blow up the bomb for him.
In Knights of the Old Republic II: The Sith Lords, Kreia digs into Atton's subconscious and holds his past over his head like an axe for the whole game, ensuring he remains loyal to the Exile. When she meets Mandalore later, she casually namedrops Revan, and then promising an answer to "the question that burns within his shell" - which likely boils down to "Why did he abandon me?" - to ensure his loyalty to the Exile.
Emphasized by an optional scene in the game - If Atton and the Exile develop enough trust between them, Atton tells the exile of his murder of several Jedi during the war, some former comrades of the Exile. The Exile accepts this and forgives Atton. Atton, having done this, confronts Kreia, and states that she has no power over him any longer. Kreia's Response - "If you thought I had any power over you in the first place then you were more of a fool than I thought. However, never forget, traitor, the feeling of guilt you had, and know that I can make you recall that feeling at - any - moment. Now, leave me, murderer". A Magnificent Bastard, indeed.
Unfortunately for Kreia, she can't manipulate droids. (She will vent her anger at T3, however.)
Up to Eleven in the Restored Content. For example, she will poke and prod at Brianna, stoking her jealousy of Visas.
A less magnificent example is Atris. She has the lowest-ranked Handmaiden join the Exile (the Handmaidens are supposed to kill Jedi who fall to the dark side). Then Atris tells the others that Handmaiden left of her own accord so that they'll kill her if she discovers her Secret Legacy and trains in the Force—which, in Atris' very narrow worldview, would constitute falling to the dark side. Atris is also the person who called the conclave on Katarr and deliberately stayed away so she could observe what was killing the Jedi.
There's no way SHODAN couldn't be one of these. Particularly in the second installment. When she first contacts you, she pretends to be the dearly departed Dr. Janice Polito, until you finally make it into her office on Deck 4. There, she will explain how her creations, The Many, are her enemies as well, and then, well, she becomes more of a slave driver than a manipulator, except that she continuous to give you cyber modules so you could be tempted to embrace her cybernetic phylosiphy. So, sure SHODAN threatens you to accomplish the tasks she gives you, and she coldly insults you every step of the way, but there's no denying that SHODAN's influence is one of the scariest things about her.
Metal Sonic from Sonic Heroes fits this trope well. Despite being seen right in the beginning, he worked behind and in the scenes, and manipulated everyone to the point where he almost won, had it not been for the teams collecting the emeralds.
Dr. Eggman has been shown to be this at times in the Sonic series. He has tricked Knuckles on several occasions, tricked Tails into revealing he had a fake Chaos Emerald, and has, at one point, tricked Sonic to get to the center of a machine that would unseal Dark Gaia and break Sonic out of his Super Mode.
Master Li of Jade Empire is the epitome of Manipulative Bastardry. He pulls off a 20 yearplan(only saved from being a Gambit Roulette because he is always in control of it) perfectly, even anticipating crash sites of flyers and manipulating family Genre Savvy enough to assume he survived a blizzard after being chucked around by a deity and to still be looking for him. He knew about and relied on Sun Hai doing that. All hail the Glorious Strategist!
Final Fantasy Tactics: Apart from all his standard Batman Gambit (in relation to Ramza,) and his own plan amid everyone else's Gambit Roulette, Delita may be seen as a Manipulative Bastard towards Ovelia if you think that he never truly loved her. Duke Barrington was one too towards Rapha and Marach, even if the former realized it very early on. Zalbaag and Dycedarg could also count on Ramza's passion for their own ends.
Adachi of Persona 4 makes another unsuspecting man do his dirty work for him and manages to successfully avoid capture until the very end of the game. Somewhat subverted in that the part with the other man was a stroke of luck.
Aradia, in her case, strings along an emotionally-vulnerable woman across a Death World filled with demons with the promise of giving her a Reason - the necessary philosophy/impetus to create a new world through the power of Kagutsuchi. It turns out she keeps withholding the promised Reason because she cannot and never could imagine it. Aradia's been lying through her teeth the entire time - only humans can conceive Reasons; what she needed was the woman's faith and hope her protege, the Demi-Fiend, was receptive to her. When it became apparent that was not the case and that she was not going to win, Aradia invoked Screw This, I'm Outta Here!. To her credit, she did try and get her follower with her (possibly to keep Aradia alive), but her emotional manipulation had drained the poor woman to the point she no longer cared even about her own life.
Gravemind from Halo deserves a nomination for convincing a super advanced A.I. who's sole function and goal was his destruction to join him.
The Prophet of Truth, the other major antagonist of the series, is also an example. Much emphasis on the 'manipulative' and much emphasis on the 'bastard.' Truth is the one who kicked off the war against humanity in the first place, after finding out that humans are the Reclaimers and may, in fact, be descendants of the Forerunners (which is later shown to be untrue). Realizing that this knowledge would prove to be the Covenant's undoing, he manipulates Prophet politics into getting himself elected a Hierarch along with his co-conspirators by claiming that humans are hoarding Forerunner relics and must pay for this insult.
Sakaki of Dot Hack GU is an interesting case. Some people can see the manipulative bastardry from the beginning, others don't realize it until his victim does. Full details: Sakaki is practically mindraping Atoli from the beginning, and always turning her away from everyone and towards himself. This is very similar to the Orochimaru gambit of taking an already heavily abused victim, and then twisting them around your little finger. He even then admits to the whole thing fully aware that Atoli is in ear shot, but unable to do anything about it.
Dimentio of Super Paper Mario. At first he appears nothing more than an amusing little henchman, but, particularly in the endgame, it becomes clear that he's manipulating both sides of the conflict to further his own ends, playing off each side's desires as well as the prophecy itself. In fact, some Epileptic Trees concerning him even go so far as to suggest that he wrote the Dark Prognosticus in the first place, setting up the whole prophecy from the beginning.
Touhou has Yukari, especially in Silent Sinner in Blue, or the numerous fanfics, plays this role all the time.
Sakuya: Whatever. Stop lying and give up your schemes, now. Yukari: (Which lies and schemes is she talking about? It's hard to keep track of them all...)
Seiga Kaku from Ten Desires has become this in numerous fan works. It's much thanks to her having kickstarted the plot of Ten Desires about 1400 years prior by putting the idea of conquering Japan with an elaborate immortality/religious war scheme into Toyosatomimi no Miko's head.
Seija Kijin from Double Dealing Character has also gained a reputation for small scale manipulation by having started a "societal upheaval" by tricking Shinmyoumaru Sukuna... "Small scale" because if you are a species of youkai infamous for being dishonest you need a Horrible Judge of Character, like Shinmyoumaru, for your trickery to ever be successful.
Sarah Kerrigan from Starcraft can get everyone, especially Zeratul, to do what she wants even after everyone knows she's a bad zerg. In Zeratul's case, she mainly does this by getting the Matriarch to tell him to go along with it. She takes advantage of Arcturus's sentimentality about Korhal too.
Technically, though, the biggest manipulator would have to be the ZergOvermind.
In Mass Effect 2, the Illusive Man knows just the right words to say and just the right favors to grant to ensure that you'll give him everything he wants. At least until the endgame, where Shepard can refuse to give him the Collector Base.
TIM is so manipulative that even if you don't believe his bull for a minute, you'll end up working for him anyway because almost every other source of assistance (the Council, Alliance, etc.) has turned against you just for being associated with Cerberus. Exactly as planned.
Also, there's Morinth, an asari sex demon who manipulates people into melding with her, killing them and making herself more powerful.
BioWare just loves this trope. In Dragon Age: Origins you have Bhelen, who outplays the character in the beginning, if you chose the Dwarven Noble origins. He tricks you in to believing that your eldest brother Trian is out to kill you for being a contender for the throne, frames you for killing him during a darkspawn campaign, and votes for exiling you and stripping you of everything and to be sent to the Deep Roads to DIE.
It's actually even better than that, if you go choose to go along with him and believe that Trian is out to get you - he manipulates Trian into attempting to kill you. If you express your disbelief, he resorts to the above, killing Trian himself and framing you for it. No matter what you do, Bhelen wins. Fortunately you can get your own sweet revenge at a later time if you so choose.
You can even forgive Bhelen for that exact reason, word for word. Bhelen and his assistant will be shocked but pleased that you admit that he played by the rules of Orzammar unfair and square.
Fontaine from BioShock. Three words: Would you kindly?
Michael Thorton of Alpha Protocol is stated in the intro to be hired into the titular organization due to being this. If the player is good enough at manipulation and alliances, Michael can even ascend to Magnificent Bastard levels.
Bob Page from Deus Ex creates a plague to infect most of the United States. Having also created the vaccine, he brags about how much power and manipulation he has over even the most powerful people.
By extension, Walton Simons is head of FEMA. During an emergency, (such as the one created by his boss's plague), Walton Simons gets to take control over most of the government, overstepping even the president of the United States. He's apparently such a manipulative bastard that there are casual NPC conversations about what a swell guy he is.
In Human Revolution there exists CASIE augmentations that give its owner an enhanced ability to read a person's reactions and exhale resistance lowering pheromones. Activating this aug turns Adam Jensen into a player controlled Manipulative Bastard.
Zhao Yun Ru actually manages get the better of Adam Jensen with a reasonably convincing Damsel in Distress impression. There is also speculation that Megan Reed is this, along with Femme Fatale, especially given the post-credit ending.
Bob Page, from the first game, is shown to be this back in 2027, from what little we see of him. the post-credit ending has him happily welcoming Megan in joining him in his efforts, and insisting that he be called by his first name. In The Missing Link, an email sent from him sent to a concerned researcher about the ethics of the projects being undertaken shows his skill in writing a heartfelt letter, and the post-script has him playfully telling the researcher to call him Bob, along with a smiley face.
Albert Silverberg of Suikoden III is also a Magnificent Bastard, given that he manipulates everyone into the events of the game just to show the world that yes, he is indeed a Silverberg and improve his reputation of being a genius Chessmaster. Then he casually derails the whole thing and waltzes away, leaving players to hope that a future game will let them get their revenge.
Suikoden IV has Graham Cray, who turns the entire country of Kooluk into his Unwitting Pawn in order to flush out and reclaim the Rune of Punishment.
Another example from IV is the elder of Na-Nal. After you fight some Kooluk soldiers trying to liberate the island, he captures you and reveals that he's allied with Kooluk, then forces you to go and steal a remedy from the Hidden Elf Village so he can score even more points with The Empire by healing the soldiers you wounded. Unfortunately for him, it turns out the Elven Elder is an even bigger bastard who predicted Na-Nal's elder would do this and lets you steal a poisonous 'remedy'. Na-Nal's apparent betrayal does NOT go over well with the rest of Kooluk's occupying forces...
In Suikoden Tierkreis, it turns out that Danash VIII deliberately engineered the tension between the Magedom ruler's multiple wives. The three consorts are constantly competing for their husband's attention and affection, and thus go out of their way to prove themselves the one willing to do the most to support and strengthen the Magedom... leading them to do things like turn their children into tools.
In both Final Fantasy II and Dissidia: Final Fantasy, The Emperor is a Manipulative Bastard who frequently approaches magnificence, in his original game wheeling and dealing with God and the Devil and winning, and in Dissidia, playing every side against the other in a ploy to rule all of existence. It's very late in the game when the other villains figure out his plans in their entirety and still can't stop him, the heroes never figure them out properly. But the most interesting twist is that this is integrated into playing as him in Dissidia — his playstyle is called "Trap Master", and is unique in that it revolves around forcing his opponent into traps or into situations where they cannot stop his virtually undodgeable Charged Attack from executing. In other words, in order to use the Emperor effectively, the player themself has to be a Manipulative Bastard!
Kyrie: Nyaha~n. Why is it that I feel like I'm not being praised one bit?
During a Super Robot Wars Compact 3 scenario, The Mariemeia troops then says that they trusted those people too much but that's fine since there's enough firepower here anyway to get Mariemeia back. To their everlasting regret, they find out that they're absolutely wrong. Heero note that it's over and Quatre says that even now, there are still people that cannot let go of Dekim's ambitions. Folka says that's probably not it, Mizal probably manipulated and incited them into taking action. Zechs Merquise asks if this Mizal is someone who was the mastermind behind this and Shou Zama says that if they don't take him out, then incidents like the Mariemeia uprising could occur again in the future.