Thief: Take a closer look at that contract. Black Mage: What, you mean this part here? Ahem "Satisfaction guaranteed, or your treasure back"? Thief: Yes. Now really concentrate on that line. See that harmless dot of ink between satisfaction and guaranteed? Black Mage: Barely... what the —! You magnificent bastard! Thief: I invented it. It's called "super ultra fine print". I own the copyright, you owe me a quarter just for reading it!
Dr. Light in the Bob and George webcomic seems like a complete idiot from the beginning. He made all his robots for mundane household chores. and Never believes Dr. Wily is evil or believes Wily has amnesia after two times trying to take over the world. However when the massive robot Gamma is destroyed Well just see
Thief of 8-bit Theater. In a team full of bastards, Thief is the magnificent one. He has total control over the team and all its assets, (and those of anyone he meets) due to his extremely convoluted and loophole-laden contracts. He is capable of stealing anything from anyone that isn't bolted down and on fire (and has broken that distinction at least once), and once stole The Lich's soul out of its gem with nothing but logic (and can cause aneurysms with the same method). And to cap it all off, he stole his own class change from the future. Case in point: Black Mage's response to Thief's Super Ultra Fine Print.
Arguably, the strip's creator, Brian Clevinger. He not only planned out a single gag five yearsin advance, but he also planned the events of the entire strip so that the Butt Monkey that is the Onion Kid eventually becomes the damn-near-omniscient Jerk Ass that is Sarda.
One more for you: Look at this. Here is the result. He lampshades it too; the second strip is called "Longest Set-Up In Webcomic History.
Then there's his ability to deal with the treacherous viziers. It's an Elven court. It's all viziers.
Not to mention Bun-Bun, especially during the Holiday Wars arc — "Well-a-ho-ho-freakin'-ho. Are we in for a year of great holiday fun or what???" Too bad his shadow was such an Unwitting Pawn...
Though Torg's contingency planning isn't as tight as this trope requires, he still managed an impressive enough streak of Magnificent Bastardry to continue manipulating criminal overlords who believe him to be Obfuscating Stupidity, and remain completely off the radar of the criminal overlords he's actually gunning for.
Aldran of anti-HEROES. There's many examples, but this comic can be taken as proof all on its own.
The character Ki, from Harkovast. He enjoys lengthy, cynical inner monologues. For example, his philosophy on heroism is an interesting one!
Dominic Deegan has several: The Infernomancer, his demonic patron Karnak, and, at least some of the time, Celesto Morgan and Jacob Deegan (the latter two sometimes act more like Worthy Opponents, too honorable for true Bastardry). Helixa might be considered one, too, and Dominic himself has certain tendencies in that direction, being at times insufferably smug about his abilities, and given to manipulating events to suit his interests (see especially the Snowsong story arc).
Shojo: What about you, halfling? Any complaints about how I run my kingdom?
Belkar: Complaints?! Dude, you make paladins clean your cat's litter box. You're my hero.
The IFCC, a trio of fiends playing some kind of elaborate game with an unknown goal, are manipulating their way forward so slickly they must know exactly what they're doing even if we don't. Anyone managing to make someone make a Deal with the Devil even when they are Genre Savvy about the trope needs to be one heck of a manipulator.
General Tarquin is always on top of what happens, never rattled, and Dangerously Genre Savvy to the point of subverting Narrative Causality to his will. What he's actually doing is perpetrating an Illuminati-style conspiracy with his adventuring companions over the entire Western Continent, ensuring that rule of every nation will soon be in the hands of six people. He's got it all planned so that he'll get to play the villain for a few decades before a hero inevitably stops him — getting to live as a king and then live on as a legend, since he's bound to make such an epic story and Evil Is Cool. After he explains this to Elan, causing him to run away in terror, Tarquin just stands there...and smoothly takes a drink.
Schlock Mercenary has General Levaughn Matsui "Hugo" Xinchub, a magnificent bastard who controlled pretty much everything for quite a while, until outdone by Tagon, a magnificent bastard in his own right. The true mark of Ximchub's magnificence was in becoming King of the planet he was exiled to, and escaping various plots by faking his own death.
But, no one compares to Petey when it comes to bastardry magnificent.
Charlie, from Erfworld, is laid out to be the Magnificent Bastard of the Wargame world of Erfworld. However, it turns out that Parson is too alien and unpredictable to make his plans work, just because of how differently Parson sees his world (as a Wargame world, while its inhabitants only see it as "world"). More recently, as Charlie thought he was being clever in his mindgames against Parson, Parson showed him that he discovered more than Charlie out of the deal (namely that Parson's Mathamancy artifact could predict the future).
Well, extrapolate statistical probabilities, at any rate.
Seth from Sorcery 101 definitely counts. At one point, he fingered a woman he was fighting. While she had the heel of one of her stilettos lodged in his skull.
And won the fight because of it.
King Radical of The Adventures of Dr. McNinja has managed to reach this status at the end of the "Doc Gets Rad" arc. He manages to trick the Doctor into disposing of his former nemesis, who was the only entity (supposedly) who could help the Doc catch him. And he did it RADICALLY.
Tarvek Sturmvoraus of Girl Genius. When Big Badpossessed another powerhouse and they switched without any warning, he played them both for hours, in such a way that he would be not only alive, but on the winning side whoever wins. Later he instantly made up to his underling he riled into hating his guts for years in such a way that she wasn't formally subservient to the Big Bad any more, he could rely on her assisting an operation saving his life, and she was blackmailed into silence about a fact that could treaten the legitimacy of his authority. While feeling himself, ahem, the prettiest frog in this entire pond!!.
Ostensibly quite uselessZola, grand mistress of Obfuscating Stupidity to such a degree that the Magnificent Tarvek (as well as Gil) considered her a mere Damsel Scrappy for years. When she showed up again in Mechanicsburg as a figurehead "Heterodyne" for some conspirators, she told Gil outright that she uses Obfuscating Stupidity, yet not even the readers saw it coming when she single-handedly knocked out every single one of the protagonists and curb-stomped the only one to regain consciousness. When she re-awakened the Big Bad and got Strapped to an Operating Table for it, she managed to Xanatos Speed Chess her way out of literally losing her mind and into holding a copy of the Big Bad prisoner in her head. As of the time of this writing, she was last seen successfully convincing another copy of said Big Bad that she is a copy as well.
In the main story she's recently proven that she belongs here with The Reveal that she had her daughter, Kalki, through the Jaal'darya in secret and avoided her mother finding out and to top it off the "father" is one Mel'arnach Val'Sarghress!
Nickolai Alaric of TwoKinds. He played Xanatos Speed Chess so well that even his own death couldn't derail his plot, and was indeed factored in as a controlled variable. All to right a wrong against his best friend. Not to mention he's a charismatic, likable rat bastard, too.
Homestuck has several notable examples: Vriska seems to be going for this, but is actually really bad at it: not only is she extremely NOT charismatic, but she can't actually manipulate anyone without resorting to using her Psychic Powers, is constantly Out-Gambitted, and never really accomplishes anything.
Terezi, on the other hand, doesn't need any psychic powers, she can manipulate people into doing whatever she wants just by being skilled at pressing people's buttons, and she's frighteningly good at it. She even managed to trick an omniscient being into carrying out a revenge plot for her. Of course, being able to read minds probably helps.
An example: when he plays chess, he doesn't react to his opponent's moves. He gives his opponent all of his moves at the start of the game, and still wins.
Some would contend that Hussie himself is the greatest of the Magnificent Bastards. All of his appearances lead into each other across massive swaths of the story, and every single thing he says becomes true anyways, and yet he is an actual living character within, AND YET writes the story. From within the story. He takes the paradoxical nature of Homestuck's timeline to another level entirely. Not to mention the fact that his death is a major storyline point, and as he is creator of said storyline within the comic, his death is going to become infinitely more complex by the end.
Oh, and that he takes pleasure and pride in trolling the readers.
Wizard of Accursed Dragon. He's got brilliant planning and is ridiculously resourceful. He seems to be able to escape everything and has enchanted robes to protect from stabbing. (People try to use swords on him a lot.)
Ariana of Grrl Power. She is essentially the PR rep and lawyer for a bunch of superheroes and the government agency they'll be working for, so she'd need to be one to do a good job. By the press conference she's showing just what a strategist she is.