Tower of God: Koon Aguero Agnis. Despite being a mere Regular, he is a guy that makes experienced Rankers of the Tower despise him so much that they would even help his enemies. Just that these enemies are actually his friends.
Jordan from Skins is a rare female example. She knows what makes her team mates tick and uses her werewolf companion's need to protect his substitute pack to manipulate him into joining her on a dangerous mission.
MAG-ISA — Love is an easy emotion to manipulate... how sad.
Dominic from Dominic Deegan. Hell, just look at the image on the comic's main page!
The eponymous girls at M9 Girls! are the unwilling subjects of Professor T.X.'s experiments. It can be argued that he has manipulated them into agreeing to the experiments.
Tohya Miho from MegaTokyo does this with varying levels of success.
Miho is an interesting (and arguably realistic) example, because while the impact of her schemes has been truly dramatic she is forced to admit that she actually ended up achieving the opposite of her true objectives. Her Manipulative Bastard actions in the Endgames prequel similarly end in failure, when Piro plays her own game back at her.
While some view Maytag of Flipside as a Purity Sue both inside and outside the comic, others view her as a frighteningly powerful Manipulative Bastard.
Mike from College Roomies from Hell!!! is a good example. Physically, he's about evenly matched with roommates Dave and Roger — but mentally, he's always two steps ahead of them. Mike can accomplish almost anything by manipulating others' actions, and he seldom betrays any affection for people other than his sister Blue and girlfriend Marsha. He can even see through the devil's mind games while being tortured in Hell.
More recently, April — once the nicest character in the strip — has let her doomed love for Mike drive her into becoming a Manipulative Bitch. In a way, she's his opposite: while Mike only falters on the rare occasions when he loses his cool, April is at her scheming best when she's most bitter and desperate. After one series of lies so brazen that it killed her conscience, there was no turning back.
Priti of Snowflakes has all the makings of a brilliant political strategist, or so she would have you believe. She's very good at manipulating any given situation to her advantage, but she only sticks around for as long as she's getting results, meaning that she never stays friends with anybody for very long. And recently, the other children have started to employ the same methods right back....
Her ancestor, Mindfang, meanwhile, was far more adept at it than Vriska was.
There's also Diamonds Droog from as early as the Intermission, who used some spectacular Mind Screwyweird time shit to take out Trace along with Doze. Unfortunately for him he didn't consider the full effects of whacking Clover with a newspaper . . .
Doc Scratch takes the cake, though. Despite making it very plain that he intends to summon an immortal demon to destroy the universe, he is still able to manipulate nearly every single character in the comic into furthering his plans. He is even able to do this without lying (except by omission, which he claims doesn't count) and being very upfront about the fact that he's manipulating everyone. This is why it's unwise to challenge The Omniscient to mindgames.
Xykon from The Order of the Stick definitely displays shades of a Manipulative Bastard at the end of Start of Darkness. He uses Redcloak's guilt and unwillingness to admit his mistakes against him to effectively turn the goblin cleric from a semi-loyal follower to a willing slave. Xykon notes with no small amount of satisfaction that Redcloak will continue to operate in his interests even when the lich can't supervise him personally because doing otherwise will force Redcloak to admit he killed his baby brother for nothing.
However, this was recently turned on its head with the reveal that Redcloak's been lying to Xykon all along about the true purpose of the Ritual, playing the spineless servant and suffering every indignation, all in order to manipulate Xykon into helping carry out a plan that doesn't help him out at all.
Tarquin has made a career out of this trope, playing off entire empires against each other for personal gain. He manipulates almost every character he comes into contact with - especially Nale, who obviously considers himself a Manipulative Bastard in his own right.
The Head Alien from the Walkyverse. He has the advantage of knowing the protagonists inside and out, being responsible for their powers and knowing them since birth because of it, and therefore has the advantage of having a reasonable idea what it takes to shock them or make them angry. (Granted, he does play favorites, making secondary characters difficult for him to deal with.)
Bestseid, a parodic cross between Darkseid and a PR guy. He's a master of making you believe and feel what he wants.
Apparently a feature of the Strakoistrat vampires introduced in "The Circle". When the Vrykolakas vampire Urja goes to kill the Strakoi Dr. Vistuvius for betraying the Vrykolakas by helping the Lysinda Circle (yet another group of vampires), Vistuvius manages to use his last words before being destroyed to say something that forces Urja to spare him — and she remarks this was only to be expected because he's a Strakoi. Also, when he gets the chance to explain himself, he plausibly claims that he was in fact betraying the Lysinda Circle to the Vrykolakas when he appeared to be helping them, and the Vrykolakas were being stupid in not realising what opportunity he was deliberately offering them.
Ashley: It's like, you could have a sandwich? And he'll want to eat the sandwich, but he won't ask you for it. Instead he'll say or do something sneaky that makes you want to give him the sandwich, all while thinking it was your idea. And then? He eats your sandwich.