Ra's Al-Ghul, who, out of all the Batman villains, poses the biggest threat globally. He too, like The Joker, has pulled almost every single plan and gambit one could think of for his final goal of wiping out ninety percent of the world's population. Add his polite exterior and cunning mind, and you have one Batman villain who is not to be trifled with.
As of the New 52, the The Riddler qualifies. Zero Year portraits him as the mind behind Wayne Industries, serving as Philip Kane's consultant. In order to secure Philip's position after Bruce's return, he hires the Red Hood Gang to dispose of the latter, knowing well that the former is a member of the gang and has to comply. When Philip threatens to kill him, he nonchalantly reveals he is aware of the metal piece inside Philip's head and uses a giant magnet to incapacitate him. Then, he causes a massive black-out just before a hurricane hits the city counting on the GCPD to unwittingly give him complete access to every computer system in Gotham by bringing the light back. To be sure Batman doesn't interfere with his plan he also manipulates the desperate Doctor Death by funding his ethically dubious research in order to provide a distraction for the Caped Crusader. And the best part is that he succeeds, and hundreds of people drown in the hurricane as a result. What truly makes him worthy of this trope this time is the fact that, at least for now, he has never shown signs of being a Smug Snake, or losing his temper even when things didn't go as he predicted.
Black Panther is quite likely the biggest in Marvel (sometimes). Every storyline during his longest run (under Christopher Priest) boiled down to "a bunch of really smart guys have a bunch of really smart, well-thought out, creative plans... that Panther anticipated and is manipulating to his own ends." It's doubly impressive because almost all of Panther's adversary are Magnificent Bastards themselves.
Lex Luthor, of The DCU. Since the eighties, he's been well entrenched in Magnificent Bastardry. He's run the gamut from crime boss to respected billionaire, to President of the United States, and despite every set back, has always managed to have the charges dropped and kept on rolling. Perhaps the best demonstration of this comes in The Black Ring, wherein he outthinks, outplans, and outfights every major contender for the title of DC's greatest villain, briefly obtaining the power of God.
Loki, Marvel's expert free-form, improv manipulator. Not only does this guy play the big boys in the Marvel Universe, this is a guy who regularly improvises the end of freaking nine worlds armed primarily with mischief and his lying tongue. And he's brought about Ragnarok multiple times. How many baddies have the chops to pull that off? He also lies regularly so well that no one can tell his lies from truth. Loki almost always gets what he wants. He's one of the few beings to have made a deal with Mephisto and come out on top.
Vril Dox II from L.E.G.I.O.N. (a modern-day "prequel" series to the Legion of Super-Heroes), a slick Insufferable Genius, orchestrates the total disruption of two planetary governments in pursuit of justice in just the first six issues. He's one of the few people that his genetic "father" Brainiac fears for a reason.
Doctor Doom is a perfect example in the Marvel Universe. Through a lethal combination of magic, technological prowess, and manipulative brilliance he's been their definitive supervillain, and the Big Bad of more crisis crossovers than can conveniently be counted. When a Norse God and the Devil both consider you a Worthy Opponent you qualify in a major way.
Wilson "The Kingpin" Fisk. No matter what the various heroes of the Marvel Universe throw at him, Fisk will always find a way to reclaim his empire, and make anyone who challenges him very sorry in the process. We've seen him rise and fall and rise again, all without ever losing the gravitas that made him The Kingpin of Crime in the first place.
Namor, the Marvel king of Atlantis and on again off again super villain can pull this off on occasion. Like when he joined the heroic "Illuminati" of Iron Man and Mr. Fantastic, and the villainous Illuminati of Doom and Norman Osborn immediately after.
Cyclops has become this over the years. One great achievement was bringing back Dracula to let him kill his own son and afterwards bluff him so good that Dracula acknowledged him as an equal and retreated. But his biggest plan that worked out in the end was bringing back the mutants via the Phoenix Force. It created the nowadays infamous Cyclops was right!
Thanos of Titan, another example from the Marvel Universe, and arguably the quintessential one, at least for the company's cosmic landscape. A premier mover and shaker in many important storylines (if not the main focus altogether), he has a knack for successfully manipulating both sides of the fence (sometimes both at once) time and time again, despite his true nature being common knowledge to everyone.
General Wade Eiling from Captain Atom. First, he framed Nathaniel Adam for drug smuggling, mutiny, and murder, when in fact Eiling had been secretly running the conspiracy responsible for those crimes. Then he talked Adam into participating as a guinea pig in the "Captain Atom Project", which led to Adam's apparent death. Then Eiling married Angela Adam, Adam's "widow." Then, when Adam rematerialized eighteen years later, now possessing superpowers, Eiling was able to talk him into masquerading as a superhero to spy on the Justice League as part of the Captain Atom project, by telling him that this would give him the opportunity to clear his name, and reconnect with his children, who thought of Eiling as their father. Even after Adam did prove his innocence, he never uncovered Eiling's involvement in the frame-up, and continued working for Eiling. And this is just the tip of the iceberg. What makes this especially impressive is that Adam is very smart, and is no slouch at political intrigue. Eiling returned in a Suicide Squad miniseries, faculties intact, where he revealed that he'd manipulated every aspect of Rick Flagg's life and used him in a coup to take over the team. Unfortunately he was running the gambit against Amanda Waller, who appears later on this page for very good reasons.
Tao of WildC.A.T.s and Sleeper. Genetically engineered tactical supergenius turned nearly unstoppable crime lord, Tao wins fights just by opening his mouth - by the time he's done with you, you'll probably have signed up with him. (Failing that, you'll be mindwiped, in a coma, or have been shot by your own allies - going up against this guy just doesn't pay.)
Spider-Man villain Roderick Kingsley, the original Hobgoblin, managed to trick Spider-Man and the Kingpin into believing the Hobgoblin was deceased Daily Bugle reporter Ned Leeds for a good 10 years real time before being caught. He then blackmailed the Green Goblin into breaking him out of prison, and is currently living in luxury in the Caribbean. Not bad for a guy who was originally a fashion designer. He's since begun franchising out the Hobgoblin trademark.
Bomb Queen, the StripperifficVillain Protagonist of her self-titled Image Comics book. The iron-fisted dictator of New Port City has, in no particular order: wiped out the rest of her original villain team; turned New Port City into a place where nothing is illegal in designed "Crime Zones"; stolen a government supercomputer, the powers of the demon lord Desarak and her clone Bomb Teen (the latter of which was "born" from her supercomputer); kept New Port City's mayor under her control with sex and verbal assaults, casually killing anyone standing near him when she blasts a hole through his office wall (repeatedly to the point of being a Running Gag); orchestrated terror attacks on the cities of other Image superheroes; repeatedly foiled the plots of the Government Conspiracy (which created her) to have her killed; and indirectly killed an innocent girl roped into her co-worker's attempt to interview Bomb Queen for their website. She is still a Villain with Good Publicity within her city. Outside her city, she has absolutely no protection under US law; she manages to avoid justly-deserved punishments every time.
John Constantine commits acts of Magnificent Bastardry on a regular basis, but he achieved awe-inspiring heights when, while dying of lung cancer, he risked destabilizing the cosmos by starting a war in Hell when he sold his soul to all three of Hell's most powerful lords—just so he could blackmail them into saving his life. And then he didn't even quit smoking. But the thing which truly crowned him as a Magnificent Bastard? He turned around to the three lords of Hell, the rulers of all of damnation, gave a little smirk, and flipped them off, stating rather non-nonchalantly "Up yours."
Gary Jackson. It was recently revealed that he faked his own death, entered the Witness Protection Program to escape the Mob, and is currently buying up his old company. He also has a swagger that commands respect from coworkers and fanboys in universe. The game system he created has much of his persona on display.
The Sultan Agameen from the indie graphic novel Artesia. He's handsome and dresses well - gold-threaded silk and fine plate are all the rage in Thessid-Gola this season. He is eloquent and treats his arch-enemy, Artesia herself, with respect. He is an incredible strategist and tactician... and he is protected by a bloody Dragon spirit.
Ozymandias from Watchmen. Right up until the end, he's the most beloved man on the planet, seemingly admired by everyone but Rorschach and the Comedian. Rich, handsome, a star gymnast well into middle age, and the smartest man in the world, the man's got style and class. And his master plan, which involved manipulating hundreds of scientists and artists and gets both Cold War superpowers to lay down their arms, succeeds, at least for the time being. And he survives the story, despite an assassination attempt at almost point blank range - he catches the bullet - and getting on the bad side of a virtual god.
Amanda Waller in Suicide Squad and Greg Rucka's Checkmate. Though she's occasionally played as a Smug Snake elsewhere, nobody can deny she's one of the few people capable of putting Batman against the wall. She is a heavy-set, nigh-menopausal black woman who escaped the Cabrini-Green area well after she had her children. And she is the leader of the very seriously titled Suicide Squad, capable of commanding both the fear and respect of the supervillains in her employ and staying on top of the pile in the politics game and as a vicious field agent by sheer force of personality, brute intellect, and this trope. This shouldtell youwhat kindof person Amanda is. Both Lex Luthor and Batman have long since decided not to fuck with Waller.
Maxwell Lord in the Brightest Day tie-in Generation Lost. In issue #1 alone, he comes back from the dead to mind-control two cops into shooting each other, beats Booster Gold half to death with a pipe, infuses himself with the blood of a small army of random extras, wipes the memory of his existence from the minds of everyone in the entire world (except our small band of plucky heroes), and rounds it all off with a glass of claret and a cigar on the battlements of Checkmate HQ.
Sin City is filled with manipulation but Dwight McCarthy is probably at the top of the heap. To give you an idea, in his first story arc, he was on the run form the cops, severely wounded, had no place to go, and had the Old Town girls ready to kick him out of the neighborhood or be killed by Miho. After about one page of dialogue, he got Miho on his side and had the Old Town girls not only giving him shelter but helping him get revenge on the Big Bad.
In the Sonic The Hedgehog comics, the villain Mammoth Mogul was originally conceived as one of these, but could never really pull it off. That is, until he essentially said to the heroes, "Hey, I just remembered I'm immortal. So here's my new plan: I'll live in this sweet casino I just had built, amuse myself by taking pot shots at you whenever I can, and wait for you all to die of old age. I can beat you by outliving you." You gotta love him for that.
Dr. Finitevus — he effortlessly manipulates the Guardians (including Knuckles), Dimitri, and two whole factions of the Dark Egg Legion in order to ensure that a new Enerjak can be created. And then he escapes scott free by jumping off Angel Island and disappearing into a Warp Ring with a smirk.
Given recent events, we can probably add Ixis Naugus to this list as well. Following his recovery from madness, he undertook a plan to make himself a Villain with Good Publicity by using MinaMongoose's music as a conduit for his magic, turning the distrust that the citizens of New Mobotropolis had for NICOLE following her brainwashing by the Iron Queen into paranoia and hatred. He then appeared before the public and promised to "save" them from NICOLE with his magic if they just agreed to make him their king. And it works, much to the shock of both the main characters and the readers. He's also become a master of Xanatos Speed Chess, apparently, as he's quickly managed to adapt to sudden situations in such a way that only improves the image this plan created for him. This includes defending the city from attacks by Eggman and the Battle Bird Armada, and acting as though his accidental deroboticization of Bunnie during a publicity stunt was intentional (the look on his face makes it clear, however, that he's as surprised as anyone else).
Dubbelosix fron Astérix and the Black Gold. With a James-Bond-esque chariot, and a trained housefly (with an unnaturally long life) to deliver his messages, he's a force to be reckoned with.
Julius Caesar anyone? It says a lot about the man that after years of publication and having his plans fail constantly, he is still treated as a genuine threat by both the fanbase and the characters. The fact that he is incredibly cool under fire probably helps—when confronted by two (superpowered) heroes, our non-powered villain states that "If you have come to kill me, I will have you know that I intend to sell my distinguished life dearly." You never doubt him for an instant.
Müsstler of the Iron Guard, who with a far-reaching conspiracy of power seekers (and presumably a few Well Intentioned Extremists), set in motion a plan to overthrow the Syldavian government, a plan involving replacing an academic with his evil twin to steal the symbol of the throne, this disgracing the King in the people's eyes.
The megalomaniacal Dogbert, pet of Dilbert. Though a multi-billionaire and former ruler of the world, he often works as a business consultant simply for the fun of conning people and stirring up trouble.