Goethe gives an opinion of what makes someone a manipulative bastard in the following passage from Elective Affinities. Eduard, who's married to the Baroness's friend Charlotte, has just told the Baroness that he's in love with Ottilie. And the Baroness decides to break up the love affair: "[A]s she made up her mind, she appeared to become even more sympathetic to Eduard's desires, for no one had more self-control than the Baroness. Self-control at crucial moments accustoms us to maintain outward composure on all occasions. When we have so much control over ourselves, we are inclined to extend it to others as an external compensation for all our inner privations... This state of mind is usually connected with a secret enjoyment of the blindness of others who walk unsuspectingly into the trap. We enjoy not only our present success but, at the same time, the other person's future embarrassment. The Baroness, therefore, was malicious enough to invite Eduard to come with Charlotte to her estate at the vintage season; and when he asked whether they might bring Ottilie, she gave an answer which he could take to be affirmative, if he chose."
Dolokhov from War and Peace often manipulates others during games of chance to earn far greater winnings, or to spur them into doing things they will regret later. He also seems to take some sort of perverted delight in seeing people, his social betters, strung around so easily.
Sauron in The Silmarillion. In particular, in "Of Beren and Lúthien", he tricks a loyal follower of Barahir into betraying the location of his hideout, makes the king of Nùmenor attack Valinor, which causes the destruction of Nùmenor, and shows the Elves how to create the Rings of Power, which Sauron later uses to enslave or corrupt some of the leaders of the races of Middle-Earth. All this only to fall foul of the fact that the existence of God makes being a Manipulative Bastard and/or a Chessmaster ultimately futile.
Morgoth is the epitome of this trait, almost in all literature. Creating just about all evil in the world either directly or indirectly. He CREATED Sauron from the once benevolent maiar, Mairon by manipulating his sense of order and desire to help mankind. Morgoth also manipulated Ungoliant to destroy the equivalent of the Sun and Moon and blind all the Valar for him to escape their imprisonment, which was only possible because he manipulated the head Valar's sense of good. He then went on to manipulate heroes into betraying their cities or their closest friends.
Dragons in Middle-Earth seem to share this trait. Smaug in The Hobbit manages to sow distrust of his Dwarf companions in Bilbo, despite Bilbo only talking in the most cryptic of riddles, the only thing giving him away being that he had the smell of Dwarf on him.
Nightfall Series: Prince Vladimir doesn’t need to force you to do anything. He can convince you to do exactly what he wants you to do, while you think it has always been your idea and you are in full control.
Shift from The Last Battle demonstrates his Manipulative Bastardry multiple times just in his first few scenes. He gets his "friend", Puzzle, to do whatever he wants through a combination of guilt-tripping and playing on Puzzle's insecurity/low self-esteem (which are a result of the way Shift treats him in the first place).
Rasheed from A Thousand Splendid Suns by Khaled Hosseini. He's a total tyrant who sexually abuses his wives to gain sex from them, while convincing them that without him, they'd be better off (which became especially true after the Taliban took over).
In his novel And the Mountains Echoed, Adel's father is a warlord who gentrifies the village and oppresses the townspeople. He pretends to support organizations such as healthcare facilities and schools while funneling money through them and gaining respect from the people.
Long John Silver from Treasure Island. While lacking the style needed to be a Magnificent Bastard, he fits this trope perfectly; acting so charming and likable that one can easily forget that he's in fact a ruthless, murderous pirate. His fondness for Jim Hawkins is particularly of notice, as even in the end it's never made clear just how much of their relationship was genuine and how much was manipulation on Silver's part.
Ellsworth Toohey from Ayn Rand's book The Fountainhead. Here's a man who holds to the Strawman Political philosophy that no one should ever achieve anything great, and he does everything he can to make people feel so insecure to be anything but a mass of mediocre and dependent "second-handers." He has a well-developed Backstory to show that he's been growing into this role all his life, and he gives a Breaking Speech to Peter Keating that explains all his motivations and goals.
What makes him even more Manipulative and Bastardly is that he doesn't genuinely believe this himself: rather, he realizes that people who lack a sense of the greatness in life are easier to control. (As witness the way he sabotages his niece's chances for a fulfilling career and a happy marriage.) Toohey is driven only by the desire for power over others, like the Party in Nineteen Eighty-Four. (In fact, both Orwell and Rand stated that inspiration for the antagonists came from observing the very worst tendencies in contemporary socialists and taking them to their logical conclusions.) Why does he do all of this? Because he knows that he is not and will never be one of the greats, so he tries his best to ensure no one else becomes great to feel better about himself. As Ayn Rand put it, he is "the man who couldn't be, and knows it".
Stephen Norton in Agatha Christie's Curtain: Poirot's Last Case is largely based on Iago. The manipulations quickly reach downright ridiculous extremes bordering on full-blown Gambit Roulettes. It often takes little more than a casual remark on Stephen Norton's part (or on the part of any of the dozens of people he uses as unwitting proxies to voice his 'suggestions' to the people involved, both victim and murderer alike) in any given conversation to set a complex chain of events into motion that will lead to someone getting killed shortly afterwards. Norton is actually so good at this, that even Poirot knows that it'd be impossible to ever him get convicted of any crime whatsoever. So Poirot decides to just kill Norton instead.
Abelard Lindsay and the other Shaper diplomats in Schismatrix, but also Lindsay's untrained rival Constantine.
Raistlin Majere in Dragonlance is very good at The Chessmaster event-manipulating (he earns his title as 'Master of Past and Present' in more than the time travel sense) but arguably even better at using people, effortlessly twisting his brother's love to his own purposes, maneuvering apprentice-Bastard-in-training Dalamar into both hating and worshiping him, manipulating guileless kender Tasselhoff into achieving several of his goals (though he screws up others) and playing (and almost always winning) mind-games with the heads of the Orders of High Sorcery, Fistandantilus, and the Dark Queen Herself. His crowning achievement, however, is his protracted seduction minus any sex (losing her virginity would cause her to lose her powers) and subsequent cruel abandonment of a holy cleric of Paladine simply so he could use her to enter the Abyss and kill the Queen. To take her place, naturally. In a supreme bit of irony, the only reason he is foiled is because he's not a heartless bastard.
Raistlin's half-sister, Kitiara Uth Matar, also qualifies. Tanis Half-Elven was putty in her hands. She successfully seduced Sturm Brightblade, effectively getting a paragon of Honor Before Reason to betray his best friend. She easily manipulated her rival in love and war, Laurana, into getting herself captured. She tricked her lover Dalamar into letting her get close enough to stab him. Though she muffed the attack and failed to kill him. And she even got the best of Raistlin a couple of times.
In the Forgotten Realms series War of the Spider Queen, Danifae Yauntyrr starts as a lowly slave after her clan was wipped out in one of the common political feuds and she was captured alive as a trophy, to serve as a personal slave to a spoiled princess. Even though any other member of her group could kill her at any time without requiring a reason, she defies and antagonizes about everyone else, makes her former mistress her personal bitch, has her Love Interest shred to bloody pieces by Jaggred, makes a high priestess to end up paralyzed with self-doubt, and gets the half-demon Jeggred to defy his aunt and follow her orders instead (as she continually proves to be much more ruthless and manipulative, and thus being worthy of his loyalty). And when it comes for the reincarnated godess to chose her new champion, she spits everyone in the face by being chosen over priestesses who had served her all their lives and sacrificed everything to gain her favor.
Leland Gaunt from Stephen King's Needful Things. He's similar to Iago, but on a large scale; he takes the conflicts among people and turns them into murderous feuds. With "pranks".
He even makes sure his customers only play pranks on people they don't know well enough to realize that the prank will play on a flaw or insecurity, but know enough about to be able to rationalize the prank to themselves by denigrating the person. And then he makes his final bit of money by selling guns...
Honor Harrington is positively awash with this types, given the series somewhat political bent, especially in the latest novels.
One good example of the cold and ambitious Manipulative Bastard would be Solarian Vice-Admiral Luis Rozsak, who is also The Chessmaster, and has absolutely no qualms about bending almost everybody to do his bidding. Surprisingly he isn't a villain, at least technically: he's a rather personable guy, and his goals are mostly noble, so he's actually more of a Well-Intentioned Extremist.
The same series also subverts this trope with Havenite secret agent Victor Cachat, who fits the same analytical type to a T, but it is only ONE part of his otherwise genuinely kind and meek personality, and manifests itself only when he firmly believes in its necessity.
Actually, Sansa had inklings of this from the beginning. She's said to be good at putting up a false front and lying to others right to their faces, so while she's caught more than a few times ( Sandor and Cersei tell her "learn to lie better, kiddo"), Littlefinger just has to pass his best manipulation techniques onto her...
David, the aforementioned 'Ani-Traitor', also falls into Manipulative Bastard territory, coming closer to wiping out the Animorphs than the entirety of the Yeerk Empire in his trilogy. He goads Jake into fighting a battle he cannot win, manipulates Ax's ignorance of alarm clocks and Rachel's opinion of him as a robber to lure Rachel into another trap, and turned the entire Berenson family into puppets by pretending to be recently-hospitalized cousin Saddler. His return in #48 goes even further, working the "The Reason You Suck" Speech overtime in his attempt to break Rachel's will to fight.
But most of all, Jake, who becomes more and more manipulative and nasty as the series progresses.
Gentleman in Fingersmith by Sarah Waters. He has exceptional insight and sometimes understands a person's mind better than they themselves do, but only uses the knowledge to exploit them, for profit and for fun.
Also Mrs Sucksby. She raises Sue as a daughter, keeping her close and innocent (and making Sue love her like a mother), but the whole time planning to her being able to put Sue away and reclaim Maud, her biological daughter.
'Sticky Eye' Kawakami in Cloud of Sparrows. He raises Heiko from a village of eta, outcasts who perform disgusting but necessary work such as butchers and tanners, as the most beautiful geisha in Edo, and assigns her as a spy and assassin attached to Genji. Genji quickly cops to the fact that she's an assassin, but it turns out Kawakami had counted on this so he could reveal her background to Genji at the right moment. This sends Genji into a well-concealed Heroic B.S.O.D., which culminates in him sending Heiko to America and massacring her entire village to prevent anyone else finding out.
Sol in Warrior Cats. His voice even seems to have the power to influence other cats' minds.
In Nick Kyme's Warhammer 40,000 novel Salamander, Iagon reveals his True Colors when he manipulates Tsu'gan into not reporting his ploys. Followed up by his reflection that he has to do something about the Apothecary who knows, and later by his murdering a helpless servant.
If they have a pulse and have set foot on the planet Arrakis (Or, as it's also known, Dune), then they're probably magnificent bastards. Paul manipulates the Fremen to make them both into an army to win back the planet AND avert a jihad he sees in the future. Jessica does to (again to the Fremen) in order to survive. Baron Harkonnen does it to eventually put a Harkonnen on the Imperial throne (although in his case he never seriously considers doing it for himself. He's in it for the legacy). The Emperor himself kills off someone described repeatedly as looking like the Emperor himself (Duke Leto Atreides) because he feels threatened by him. The only people in the book who aren't magnificent bastards (or just bastards) is Gurney Hallack or dead (like Duncan Idaho. Don't worry, he gets both better and a magnificent bastard).
Leto II. There's a reason he's becomes the God-Emperor. He manages to manipulate every single human being that crosses his path, up to and including his grandmother, his aunt and his own father, all of which should have known better. Then he ends up ruling the entire known universe for 3500 years with an iron fist. To be fair, he really didn't manipulate his father Paul. It was more like winning an argument and Paul realizing Leto was right, much to his dismay.
Nigel Bishop, from the Dream Park novel The California Voodoo Game, wrote the book on Manipulative Bastardry (The Art of Gaming). An outstanding example of this trope, not least because Bishop unabashedly convinces the Gaming world he's a Magnificent Bastard, and is universally admired for it; only the reader knows the extent of his crimes, or the tone of his internal monologue, that show he's too much of a Bastard to rightly qualify as Magnificent.
Also from Jim Butcher, Martin, in The Dresden Files. Nicknamed "Mr. Bland" when Harry meets him, the guy is a half-vampire working for an anti-vampire organization called the Fellowship of St. Giles who seems to have absolutely no emotions. He says it's necessary for his work, where emotions create attachment and he has to do very bad things in order to defeat the Red Court vampires. He ain't kidding. In the end, turns out not only is he a mole for the Red Court, but he is actually against THEM as well. He's been feeding them entirely accurate information, including that which has led to hundreds of deaths of humans, to put them into a position of enough power where they would initiate an incredibly dangerous magical ritual just for the sake of vengeance. Then he manipulated Harry into being forced to kill Susan— his ex-girlfriend and mother of his child (as well as Martin's partner for about a decade)— in a way that would turn the ritual against the Reds, wiping out all the Red Court vampires in the world.Yikes.
Nicodemus also likes to do this sort of thing. Highlights include tossing an Artifact of Doom at a toddler in order to force Harry to pick it up (implanting a copy of a Fallen Angel's personality in his head in the process) and displaying a horribly-tortured little girl to try to provoke Harry into using the Sword of Faith to break a promise. (The latter of which fails; Harry immediately realizes what Nick's trying to do, and he's made that mistake before and does not wish to repeat it)
Harry's developed this as well. Witness using Lara Raith as a catspaw to destroy Lord Raith while making her think that he is her catspaw.
Speaking of Lara, this trope is pretty much the Hat of all the upper-rank White Court vampires. The lower-ranking ones are lower-ranking because they're not as good at it.
Any descendant of Kushiel in Kushiel's Legacy can become a Manipulative Bastard. They can actually "see" what it will take to get people to act in a specific manner. Melisande embraces being a Manipulative Bastard and manipulates people just because she can. Her son Imriel tries to avoid being a Manipulative Bastard but still has that ability for when he needs to use it.
Many Sherlock Holmes villains qualify and so does Sherlock Holmes himself. In more than a couple occasions he has gone as far as to emotionally manipulate, not just the villains but innocent bystanders and Watson as well, to achieve his goals. Watson notes that this amuses him greatly.
Anna from Ann M. Martin's Slam Book. She admittedly accidentally drives an unpopular girl to suicide. She feels bad briefly — but her parents assure her that oh, it's mostly because that girl was unadjusted in the first place! Right...
Rimmer Dal, Big Bad of Terry Brooks's The Heritage of Shannara series. He so thoroughly destroys Par's sense of self and right and wrong, that by the end the poor kid is borderline insane, and barely able to distinguish between reality and fantasy. Worst of all, this is exactly the result he was after, as a Par whose will is utterly shattered won't be able to prevent Dal's Grand Theft Me from going into effect. He turns this kid into The Woobie purely for his own benefit, and the kicker? It takes the Sword of Shannara (an artifact designed to expose the truth) to pierce through all the lies he's told. That almost isn't enough, because he manages to talk Par into believing he can't use it. Manipulative Bastard and Consummate Liar indeed.
In China Miéville's novel The Scar, Uther Doul is either this or Magnificent Bastard, depending on your interpretation. He knows that the Lovers' plan will get them all killed (if you believe that; arguably, that part could have been a lie too), but he doesn't want to be shown doing anything himself to oppose the Lovers, so he manipulates Bellis by giving just enough information to start a rebellion of Armada's citizens, even indulging her growing infatuation with him. Many readers fell for it hook, line, and sinker, thinking he'd become an Anti-Villain in time and end up with Bellis, and oh how wrong they were. The revelation that he never felt anything for Bellis, and was only using her, felt pretty harsh.
Mayor Prentiss from Patrick Ness's Chaos Walking series. Throughout The Ask and the Answer, he plays head games with Todd, Viola, and his own son who he ends up shooting. He could also be considered a Magnificent Bastard as he is extremely confident and independent. Starts a Big Badass Battle Sequence at the beginning of Monsters of Men. In The Knife of Never Letting Go, drags Aaron along as a Church Militant while trying to chase Todd down.
Voldemort from Harry Potter. Especially when he was younger, and charmed everyone around him into to thinking he was the hero. Everything he says is a form of emotional manipulation (guilt-tripping, flattery, fear-mongering, put-downs to lower self-esteem), it's just that he doesn't use his charm to its full extent as an adult, preferring to manipulate using negative reinforcement instead. As is repeatedly stated in the series: "Lord Voldemort's gift for spreading discord and enmity is very great."
Dumbledore. He plays people from beyond the grave, using his reputation as a kind, slightly Cloud CuckoolanderBig Good to get everyone to do exactly what he wants, playing on Voldemort's vanity and shortsightedness, Snape's love for Lily and Harry's chronic heroism. Also, what he did with Draco. He knew the kid was trying to kill him, and he knew he wouldn't be doing it if Voldemort hadn't put him up to it. Yet he still refused to confront him until The Plan he'd dragged Snape into came to fruition. When he offered to hide Draco and his family, it was already too late for him to accept.
Xanatos from Jedi Apprentice and his bastard son Granta Omega from Jedi Quest are both very effective Manipulative Bastards, specialising in screwing with their opponents' minds during combat. Xanatos is especially brutal, giving Obi-Wan a Not So Different/"The Reason You Suck" Speech after the former is forced to kill fellow student Bruck, that nearly shatters the boy's self-confidence.
In Donald Kingsbury's Courtship Rite, most Getans consider the whole Kaiel clan to be this—and, indeed, they seem to be actively trying to breed for the trait, in several ways. Within the Kaiel, Prime Predictor Aesoe is a prime example, ordering the three protagonist brothers to marry Oelita, the Gentle Heretic (against the wishes of all parties) so the Kaiel will gain influence with her followers.
Legacy of the Dragokin: All the drama in Drewghaven was a distraction planned by Man in Shadow to get Daniar out of her castle. He led the rioters to the Kthonian knights' can and sent the distress signal letter to Brittania castle so Daniar would rush to her sister's aid. Once she was gone he could dig up Erowin's corpse without interference or observation.
Later subverted when it is made clear that Deshamai really did believe that what he did was the best thing for Caederan, and still more so when he gives a really awesome speech to the court and talks them into letting Alaric and Laeshana marry.
Lord Cuncz in No Good Deed..., bonus points for being an actual bastard, as well. Garnerius arranged for his adoption and legitimation with the previous Baron of Leyen because he thought Cuncz would be easily controlled and disposed of when he was ready to make a political move against the Prince-Bishop of Bremen. Cuncz in turned played him behind the scenes, working with the Prince-Bishop to expose the Abbot's machinations and have Friuli Abbey added to his fief as a reward. When Elsabeth and Hieronymus unwittingly foil his plans to recover incriminating evidence against the Abbot, he just uses them to carry out his plans instead. And then he seduces Elsabeth by letting her seduce him as part of her plans to steal the documents from he he actually wants her to steal, for no other reason than he wanted to sleep with her!
Lissa Dragomir weasels her way out of any situation using only words. For example, she manipulates the usually strong-willed Camille Conta, a royal girl, to act as a defender to Rose's reputation. She manipulates Aaron (her former boyfriend) to get back together with her, while she truly finds him boring. This ensures the further isolation of Mia Rinaldi.
Victor Dashkov has his daughter commit evil acts behind everyone's back and even convinces her to turn Strigoi in order to break him out of a secure prison. Manipulates Lissa into trusting him as an adoptive uncle while planning to use her for his own purposes. Manipulates Rose into sleeping with Dimitri, to get them both out of the way of his plans.
In Blood Promise, Avery Lazar manipulated emotions and perspectives towards her own ruthless goals. Leads Lissa towards a self-destructive path and slowly seduces Adrian.
Companions Of The Night: Ethan, being an immortal vampire, has had a fairly long time to practice his acting skills and learn to efficiently have people act the exact way he wants them to.
Duke Selen Esrah used manipulation to start a coup. When Kasile investigated her own kidnapping, he pretended to be her greatest aid when he was truly the one she was looking for. He twisted her conclusion to frame her for treason.
Emotional blackmail is Tasio's stock-in-trade. He motivated Eric to grow a spine by faking a tragic death as Aio and then twisted Basilard's arm into completing Zettai's Bladi Conversion by first shapeshifting into Zettai's form at her most pitiful and then indirectly threatening that he might not ever become a father otherwise.
Karlax from the Doctor Who novel "Engines of War". The narration states that he has spent most of his lives manipulating others in order to achieve his own goals.
In The Treasure of the Sierra Madre,Pat Mc Cormick is an oilfield contractor who gets foreigners (who aren't covered by Mexican labor laws) to work for him by pretending to be a Comrade who's just trying to stay afloat and help some fellow working men out. He uses this to get them to work longer and harder hours, then absconds with their pay, often convincing them that the fault is with the dirty oil barons delaying payments, and to come out on another contract with him in the meantime.
The Dinosaur Lords: Bergdahl uses masterful rumour-mongering to make people like Falk and dislike Jaume. He also manipulates Falk by playing on man's insecurities, need for appreciation and feelings of guilt, and claims to have gotten a job at the Palace by blackmail.
Errastas from Malazan Book of the Fallen greatly enjoys causing mischief. The reader first encounters him in Letheras, where he has been laying low for decades to steer the politics in the city and especially in the palace, playing a major role in the instigation of the upcoming war with the Edur. The Kharkanas Trilogy shows that he is not above playing azathanai for fools, either, using Draconus' request for a Terondai as a means to get a foot into the door of K'rul's new free-for-all magic system.
The Stormlight Archive: Shallan Davar, like all Lightweavers, is a heroic version. In the first book she manipulates her way into a princess's service in order to steal a valuable artifact from her, and in the second book she convinces a band of deserters who were planning to kill her to fight for her instead.