In the New 52, The Joker has been ramped up in this regard. In the retelling of the origin of Jason Todd, the second Robin and the one who was killed by the Joker, the story is seen from two perspectives, that of Jason and that of the Joker, with heavy indications that Joker arranged events so that Jason would appear to be the prefect candidate to replace Dick Grayson as Robin to Batman, purely so he could eventually lure Jason into a trap and kill him just to get at Batman. After that, in the Bat Family Crossover, Death Of The Family, Joker returns after a year's absence and proceeds to unfold a meticulous plan that targeted each member of the Bat Family personally, so that they would begin questioning if the Joker knew who they really were and lose faith in Batman, allowing him to take the entire group down one by one.
Henry Bendix, the creator of Apollo and Midnighter, is all over this trope in the nastiest way. His amazing talents of mindfuckery let him plan ten steps ahead on any given day, but he has a special talent for screwing over his own creations: he knows where all their buttons are, and in many cases, he installed them. See The Authority: Revolution for a crowning example of this - all he had to do was prey on Midnighter's worst insecurities, and bam: one indomitable superteam dissolved, one happy family ripped apart, and the world left wide open to a fascist takeover. Sure, it's all (mostly) okay in the end, because Jenny Quantum is too awesome to stand for supervillains or parental abandonment, but Midnighter still spends several pointless and horrible years apart from his husband and daughter, unwittingly helping the bad guy. For someone with no apparent superpowers, Bendix manages to scare the crap out of some very high-level heroes.
Mister Sinister from X-Men has been the ultimate Marvel Manipulative Bastard for the past twenty years, manipulating the lives of the Summers family in particular You can blame him for the Summers' Tangled Family Tree.
Good example is also Selene, who just loves to trick and manipulates hapless teenagers, male or female alike, to do her bidding and dirty their hands in her stead. Not that she actually needs to - she's one of the most powerful mutants alive - but toying with people's feelings is just too entertaining for her not to indulge. She even tried this on The Hulk and Rachel Summers but well, everyone has their limits...
On a much smaller scale is Victor "Sabretooth" Creed, a bestial, gleefully murderousPsycho for Hire. While exceptionally intelligent and probably quite capable of executing wide-reaching plans, he's more than content to execute schemes based around one thing: tormenting Wolverine. His manipulation almost always involves turning people against Wolverine and setting up scenarios that will invariably end with great tragedy for Logan, and Creed has made his intent clear time and time again: if Logan ever finds anything that makes him truly happy, Creed will be there to make sure that Logan hits rock bottom again.
John Constantine, this bastard is ready to sacrifice some lives to save his ass (or save the world). He even tricked God to save his soul from Hell.
His dead ghost evil twin is just the same. Not only has he manipulated John, Satan and God aren't safe from him either.
Ysanne Isard, particularly in the comics. The Director of Imperial Intelligence, she served the Emperor until his death. After the Battle of Endor, Isard advised Grand Vizier Sate Pestage while plotting to make his position shaky enough that he made plans to abandon the Empire and flee to the Rebellion. In the same day, Isard had Pestage and the obstructive Imperial Ruling Council assassinated, leaving her Empress in all but name. A favored element in her plans involved capturing members of the Rebel Alliance, brainwashing them into becoming sleeper agents, and sending them back completely unaware to their superiors, awaiting the right moment to activate them.
* Carl Barks's Scrooge McDuck was a master manipulator and trickster who enjoyed every minute of it... all done in the name of teaching his nephews and grand-nephews important lessons about courage, money, hard work, etc.
Batman: Hush is going to manipulate you. No matter who and he is going to put other plots underneath the current plan just in case you don't serve his purpose.
During the Sinestro Corps War storyline in Green Lantern, Sinestro managed to manipulate the Green Lantern Corps, the Guardians of the Universe, every superhero on Earth, and everyone fighting on his own side. He assembled his own intergalactic army, created a power source run on pure fear, brought together the most powerful collection of supervillains the cosmos had ever seen, declared war on the entire universe...and lost. The Lanterns sentence Sinestro to death, thus breaking their own law against never taking a life. It turns out this was what Sinestro wanted all along — his plan was not to destroy the Green Lanterns or conquer the universe, but to create a threat so great and terrifying that they would abandon all their principles to stop it. He tells Hal Jordan and Kyle Rayner that he still believes in what the Green Lanterns stand for (so much so that he's proud to have a daughter in the Corps). He wanted the Guardians to rewrite the Book of Oa to allow Green Lanterns to wield lethal force. "The universe will fear the Green Lanterns, and the universe will be better for it." He essentially assembled a bunch of heavy hitters (Hank Henshaw, Superboy Prime, the Anti-Monitor) that the GLC (and possibly the JLA and the JSA) would have to kill in order to stop. Even Superman considers killing (which he has only done once) when Hank Henshaw tells Big Blue that he could never kill him, "To be honest Henshaw, I've never tried."
Loki. What he did after Ragnarok: he came back in a female body (which was presumably meant for Sif), started plotting with Dr. Doom behind the Asgardians' backs, tried to convince the same Asgardians that Beta Ray Bill was an infiltrated Skrull, gathered the Mighty Avengers with an astral disguise of the Scarlet Witch just to break Norman Osborn little by little (while at the same time plotting together with him), brought Bor to the future and allowed Thor to kill him so his brother could be banished, gave Osborn the idea to invade Asgard, allowed him to convince the authorities to do so by sicking the U-Foes on a rather reckless Volstagg...Then he topped himself, trying to worm back into good graces of his family, when the actions above made everyone hate him more than ever. He "sacrificed" himself against rampaging Sentry and reincarnated as a relatively innocent kid, which had intelligence and general attitude of Old Loki, but not his memories. But all of that was a scheme to give Old Loki a new lease on life with (somewhat) restored reputation, and from the beginning he arranged things to eventually overwrite Kid Loki's personality and take over.
Holden Carver: TAO is the scariest bastard I've ever met. Don't get me wrong, it's not like he's some rampaging psycho who'll rip your guts out. He's worse. TAO will get you torip your own guts out.
Holden Carver: John Lynch has been in a coma for a year, since his best friend Cole Cash shot him. Cash doesn't even remember shooting him, because TAO thought it would be funnier that way.
Surprisingly, Archie Comics has its very own with Trula Twyst, an obsessive psychologist teen with a focus on Jughead Jones. She uses her powers of persuasion (bordering on mind control) to, on separate occasions, convince him he loves her, give up hamburgers, give up his master revenge plan on her, etc. Her first appearance features her convincing Jug he likes her, just so she can get the attention of all the other boys in town for "seducing the un-seduceable".
Both Hobgoblin and Green Goblin are masters of this. Hobby was able to perform shady and illegal business practices and frame a reporter to take the fall for him, and got away with it for several years. Norman Osborn masterminded The Clone Saga and ruined Spidey's life as well as getting to be Director of SHIELD. Unlike Hobby, Norman had been under suspicion for years, if not as the goblin by Ben Urich, then as a crooked businessman by nearly everyone else.
Deathstroke from the DCU. He's not quite as good at this as others on this list — most of his targets tend to be damaged teenagers a generation or two younger than him, hardly the most challenging targets. When his powers of persuasion aren't enough to get them to work for him, he's not above using blackmail, death threats, mind controlling drugs, and Psycho Serum to force them to join him.
Ava Lord from Sin City is a Manipuative Bitch who is good enough to manipulate fellow manipulator, Dwight McCarthy.
Moonstone was an extremely unethical psychiatrist who got her powers by manipulating the original Moonstone into giving his up then stealing them. Afterwards, even though she was super-strong and could fly, emit energy bolts, and phase though walls, her ability to manipulate people was considered at least as dangerous as her powers.
In the Sonic the Hedgehog comics, we have Doctor Finitevus, who is most famous for the time he manipulated Dimitri, the Guardians (including Knuckles), and two factions of the Dark Legion in order to create a new incarnation of Enerjak, and then teleporting away from the resulting carnage with a smirk. Fortunately, Knuckles seems to have learned his lesson since then - when they next met and Finitevus tried to use him again, Knuckles kicked his ass and threw him off of Angel Island.
Finitevus's former minion Scourge seems to have learned a thing or two from him — half of his Sonic Universe arc is learning and playing off of the Destructix's secrets and emotional weaknesses, in order to convince them to work for him.
Moretti of Give Me Liberty, who manages to blackmail the Action Girl heroine into servitude, frames the Chairman of the Joint Chiefs for destroying the Apache Nation with an orbital laser, stages a Presidential coup that destroys the White House, and appoints himself interim leader of the United States.
All Fall Down: Using Phylum's voice box, AIQ Squared manipulates Pronto into selling his soul for the chance to get his powers back.
Cheshire of both Teen Titans and Secret Six counts. What's the best way to gain a good hold on a superhero (Roy Harper) with ties to two of the most influential super teams ever known (the Teen Titans and the Justice League), and a supervillain who is ostensibly considered the deadliest tracker on Earth (Thomas Blake)? Have their children. How do you plan to gain sympathy even after you've destroyed a country with an atomic bomb? Destroy a country considered to be the terrorist capital of the planet, Qurac.
Speaking of Daken... Daken cares for nothing but his own desires, and is willing to use anyone to get what he wants. He's helped by the pheromones he can emit, which allow him to toy with the emotions of people around him, and pulls off Xanatos Gambit after Xanatos Gambit. In one case, he completely takes over Madripoor by secretly supporting everyone in their bids for power after a shutdown of major utilities that he himself arranged, before putting up Tyger Tiger as a puppet, and that was just part of his master plan to get Malcolm Colcord to give him the full Weapon X treatment. And oh yeah, he had a backup plan for that (in the form of his little sister, X-23, whom he put in place by capturing her and turning her over for experimentation, then allowed her to escape through a combination of unlocked restraints and a vial of Trigger Scent) in case Colcord tried to stiff him. He did. The boy has so many plans within plans, you never know if he's genuinely being nice to you or is just setting you up.
The Kingpin is disturbingly good at this. He built himself up from a low-level street thug, to assassin, to the Big Bad behind most of the organized crime on the East Coast. He was a significant threat for Spider-Man, but he truly began to show how terrifyingly good at manipulating people he was once he became the main villain in the Daredevil comics. In the "Born Again" storyline by neo-noir comics master Frank Miller, the Kingpin finds out that Matt Murdock is Daredevil and begins a months-long plot to systematically destroy his life before finally trying to kill him, putting Daredevil through the trial of his life. He has his hands in every cookie jar, has a general in his pocket, and has spieseverywhere. Even after he's jailed, he proves very savvy at manipulating people from behind bars.