The Gord, of Acts of Gord, especially in the final book. While Gord was on vacation overseas, the person he left the store to (the Guardian) conspired with the Gord's Landlord who had been pocketing money for a while so that Gord would lose his license. When Gord found out the Guardian and the Landlord intended to sell off the property and liquidate everything, the Gord instructed some of his friends to break into his own store and take everything that wasn't nailed down. Since the Gord was still legally the owner of his store and had purchased everything inside it, this wasn't illegal. When the Guardian and the Landlord show up the next day, they find absolutely nothing, meaning they'll both lose their jobs. And they can't report this to the police, or else they'll be arrested for fraud. In the end, the Gord had the last laugh, but got out of the business and left his empty store behind.
Maffeo Servitore, of Florence, who's not coincidentally an Expy of Machiavelli.
Alfred Kleiber, chancellor of German Atlantis (=America), who manages to unite the three Germanies (in Europe, North and South Atlantis) into one great superpower.
And the New Roman emperors, who make Italy into another superpower owning lands on four continents.
Michael-lan of The Salvation War, who is able to manipulate an entire interdimensional war to position himself in control of Heaven, and his ambitions might not even stop there.
Mildly subverted by one of his motives being to prevent angelic extinction — if his "muscle" had gone about their plans unabated, they might have very well taken out his native power base and possibly himself in the process... and, if they ever decide to do kill him, they most likely will succeed.
Then Elhmas shows up...
It's to be expected that Neon Genesis Evangelion fanfiction contains a Magnificent Bastard if the author is doing his job, but Gendo Ikari in Aeon Natum Engel puts his narrative predecessor to shame; he actually seems incapable of doing even the most rudimentary of actions without dragging in a multi-layer plan.
Although given some of the other characters, both Expys and OCs, he has competition. Not enough to lose (because, hey, he's Gendo), but enough that the story becomes a Jigsaw Puzzle Plot.
On Neopets, there was one villain who was in one of those events where you pick a side in a conflict. Darigan was an early one, and he's notable in that he managed to get most of the players on his side, making him win the war. Yes, through a sob story, a villain managed to convince most of the players to join his side.
In the same part of the manual, he blows up his new body to get inside a space station commander, kills the commander and uses a spaceship captain to organize a resistance, and then proceeds to hide that resistance for years before using two superpowers against one another, arranging a mass Reverse Mole inside The Empire, stealing their superweapon, and teaming up with the Reverse Moles and The Alliance to completely destroy them. Then he just leaves, dropping in to taunt people every once in a while.
While Let's Play-ing Within A Deep Forest, DeceasedCrab said of the game's designer "I can't help but respect Nifflas for his superior bastardry. Not saying that you're illegitimate or anything, just that you're utterly heartless, dude." Note the context: DC was LP-ing Within A Deep Forest because he had previously been playing La-Mulana, and he needed a break from its aptly-named Hell Temple. So a comparison of DC's reaction to the two games' difficulty levels is a nice object lesson in the difference between Magnificent Bastardry and plain old bastardry.
Dusty is probably the rudest, crudest, most perverted and vulgar thing to walk this Earth and not be labeled as evil. And yet he's one of the most loved characters on Matt N Dusty.
Kevin Baugh in Kickassia. He instantly ends the first attack on his country by pulling a machine gun from Hammerspace, is revealed to have a sword that enables him to teleport, and when Molossia ends up conquered he uses Obfuscating Stupidity to sow dissent among the new government.
Whateley Universe has multiple ones. Ayla, at the least, is in training as one. Thuban is working his way into this position. The winner, however, is Dr. Diabolik. He initiates a beautiful, three-tiered plan in the latest story.
The ending of the Hat Films series Hat Corp has the trio reveal themselves as this. While they lost the war with Kim Richards and Duncan Jones, they were able to claim on the insurance for their base to get a fantastic new one elsewhere, without anyone else knowing this. All this was done by scamming some builders out of their money, meaning that the Sirs are able to resume their efforts for world domination later.
In X-Ray & Vav, The Mad King turns into this in Season 2 as, in the span of one episode, is able to cast doubt into X-Ray and Vav's bond and get Mogar to free him. by just talking to them. He goes further in later episodes as he's able to take back Monarch Labs by proving Hilda had no idea how to really run a company (and a conspicuous helping of puppies), win the city over and prove X-Ray and Vav incompetent and break up their partnership.