If you play Mitadake High and are a charismatic Kira, as opposed to a n00b or someone lucky enough to run into the Eyes and get their help early, you will be one of these. It's basically a victory requirement.
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.
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.
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.
Spoony is also a real-life example. Many of us, if suffering needlessly cruel Railroading would just slog on, depressed that they just got fokked as the new guy in the game who didn't pick the popular side. Spoony's response? SEMTEX. And all completely within the rules.
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.
Liz Polanski on Survival Of The Fittest V4 is becoming this. She disabled her collar, and broke a camera (which would normally lead the the collar exploding) to demonstrate that it didn't work. When Danya had another student's collar blow up because of it; she decided to destroy all the cameras she could find just to make Danya look stupid..