Prince Lucanor Giovanni from Anima Beyond Fantasy certainly qualifies. He is effectively the second smartest person in the entire setting, second only to his brilliant but insane mentor. Despite being a normal human in a setting full of supernatural beings and super powered individuals he remains one of the most major political players in the setting due to his near omniscient ability to deduct what everyone else is up to. He actively manipulates almost every other side in the setting without them realizing it.
Asmodeus, ruler of Nessus, Ninth Layer of Baator in Dungeons & Dragons. He is one of the oldest living things in the multiverse, controlling all of the Nine Hells and standing over every other devil. The gods fear him. He once instigated the Reckoning, an Enemy Civil War, just to root out the more dangerous of his foes... only to promptly step forward and force all of Baator to submit once it stopped being useful to him. His only reaction to Mephistopheles threatening to take his throne was an amused silence.
His most epic moment was likely when he first came to rule the Hells, when the Gods sent him to punish those who had sinned, signing a contract to say that Asmodeus could do as he wanted with those souls. Shortly thereafter, the Gods noticed that rather fewer mortals were coming to their planes when they died, and more were going to Hell. They soon found out Asmodeus was deliberately tempting mortals to sin, and confronted him, saying that the contract did not give him permission to tempt mortals. He simply smiled at the gods, and said "Read The Fine Print."
Don't forget that with the update to 4th Edition his status went from merely a powerful archdevil that required a full team of high level epic characters to fight into a full god.
His ascension to godhood is arguably even more magnificent in the Forgotten Realms setting, where he effortlessly orchestrates the death of a major god and consumes said god's soul.
Asmodeus' first Starscream was Baalzebul, Lord of the Flies. Baalzebul was almost as magnificent as Asmodeus himself. He was a former angel who went to hell and did such a good job taking over that he completely removed all knowledge of his predecessor's name and identity from existence. He managed to control two levels of Hell, one himself and one through a viceroy, Moloch. Add to that, he actually had Asmodeus' favor. Unfortunately for Baalzebul, during that civil war he led an insurrection that tried to take Asmodeus down. He was thwarted when Mephistopheles' troops turned on the insurrection, and then Asmodeus punished him by changing his form from that of an angel to that of a slug. Baalzebul's still the #3 guy in Hell (behind Asmodeus and Mephistopheles), but looking like a slug pretty much demotes him from Magnificent Bastard to The Chessmaster.
An arguable example is the Demon Lord Dagon. Like other Demons, he is Chaotic Evil. Unlike other Demons however, he is intelligent, rational, and above all, patient. He is reported to be the first Demon Lord spawned from the Abyss, and uses his vast knowledge to manipulate the minds of mortals and demons alike. Oh, and his alliance with Demogorgon, which makes him seem like The Dragon? It's heavily implied that their alliance is part of a greater scheme in Dagon's benefit, and in fact he plays a big role in the continuing feud between Demogorgon's Split Personality issue. (He only speaks to one of Demogorgon's two minds when giving advice.)
And if you look at him, you become terrified of the sea. Did we forget to mention that Dagon lives at the bottom of an Abyssal ocean? His very existence insulates him from retribution.
The entire race of Yugoloths are would-be Magnificent Bastards. Not would-be as in smug snakes, would-be as in it's tough to be remarkably magnificent when everyone else thinks and plots just like you do. Less well known than the Devils and Demons, they're Neutral Evil as opposed to Lawful Evil like the Devils or Chaotic Evil like the Demons. The Yugoloths' main stronghold is The Crawling City, a city grafted onto legs that walks around the mountains of Gehenna. Prophecies say that the Blood War will only end once the Crawling City directly intervenes in it.
Spoiler, The prophecies are wrong in this case. In the Forgotten Realms setting, Asomdeus ended the Blood War by pushing the Abyss to the bottom of the Elemental Chaos with no help from the Crawling City. He is a Magnificent Bastard!
Another possible Magnificent (in this case) Bitch would be Lolth. She may seem insane but like Tzeentch, she is either that or very sane. She favors chaos and looks out for too much cooperation between drow but at the same time, she makes certain that they do not cause too much chaos. She looks on those who cause chaos in normal drow society with favor and she doesn't limit herself to evil ones, at that. She also orchestrated the deaths of several of her own children, to ensure that she'd remain as the sole deity of the drow, also being one of the main factors that could have lead to the Spellplague. When she went silent to the drow prayers for a long time, she used this time to reestablish herself as a new greater deity, moving the Demonweb Pits away from the Abyss and confirm it as its own plane of existence. YMMV on this one, but you have to admit Lolth is one hell of a player in her own.
The Dark Powers of the Ravenloft setting can be Magnificently Bastard-ish when tormenting their darklord captives, playing off weaknesses and hang-ups that the darklords won't even admit they have. Many fans of the setting remain convinced that the DPs are on the side of the angels, simply because it's villains whom they're hassling with such expertise. The fact that they work in secret rather than stepping onstage doesn't disqualify them from this trope, as their resulting mystique more than makes up for it.
Some of the domain lords, themselves, also qualify. Azalin, Harkon Lukas, and Strahd von Zarovich probably rate highest in fan admiration for their scheming, as does the non-darklord Gentleman Caller.
Cleon Zhunastu, founder of the Third Imperium in Traveller. He actually did better then Palpatine because his Empire lasted for more then a thousand years. He manipulated dozens of powerful men and thousands of planets into forming the Third Imperium.
Hanse Davion from BattleTech. While he reshaped military thinking within his life, he will probably best be remembered for his acts of Magnificent Bastardry. The first being where he ordered the court martial, exile and stripping of name from the son of his Intelligence Secretary - and best friend - as a part of an elaborate ruse to plant him into another state's intelligence network. So successful was this gambit that in the subsequent war (Which Hanse started at his own wedding) he captured more worlds in two years of fighting then his predecessors had in the last two hundred, all but crippling the state and driving its leader to insanity. Why did he do it? As an act of revenge against said leader who had tried to kill Hanse and replace him with a doppleganger.
While on the subject of BattleTech, let us not forget Ulric Kerensky. Even when introduced as 'merely' the Khan of Clan Wolf, he already comes across as this; once voted into the position of ilKhan and forced to lead an invasion he's essentially opposed to, he manages to ever-so-subtly sabotage it without ever committing an outright act of treason (most notably by playing on the vanity of the other leaders and letting them get hoist by their own petards when they're too full of themselves to ask for advice or instructions), ultimately culminating in a fifteen-year truce — and then, when later challenged over it, sets into motion a plan to cripple the Clan pushing the hardest to resume the invasion while making sure part of his own Clan survives to keep defending the Inner Sphere in the future, even though it will cost his own life among others. Throughout it all and even posthumously he's never depicted as being anything less than completely in control and on top of events.
Also Sun-Tzu Liao. He turned his crippled state (Courtesy of Hanse Davion above) around in the space of a few years, abused his elected position as the new First Lord of the reborn Star League to allow his nation to legally annex a breakaway state, reclaimed more then half the territory his grandfather lost under the pretense of "Peacekeeping" operations and forged a three-way alliance amongst other dissafected nations. There's (circumstantial) evidence that he even nuked his own capitol to serve as a propaganda piece to provoke hatred of his enemies. In the end he fakes his own death to ascend to the level of godhood in the eyes of his people. In many ways he acts like Hanse Davion, and he noted that he was using techniques he had learned from studying Davion.
Tzeentch of Warhammer 40000 is a literal god of scheming who lays plans that take millennia to pay off. Whilst we're in the same universe, the Alpha Legion are, most terrifyingly, an entire army of Magnificent Bastards, even before the Horus Heresy (with the exception of Bale and Carron, but we don't talk about them).
Tzeentch is probably enjoying it. He is literally the god of scheming. He cares not whether the schemes will work or not. He finds it very amusing to mislead his own followers to fulfill his own, incredibly far-reaching plans, and his own plans tend to be contradictory and ultimately nonsensical. Infact, despite what he might want you to believe, he doesn't have any ultimate goal other than scheming itself, and if he did, he would cease from existence upon reaching it, as his whole purpose is to scheme.
One of the problems of the 40k setting is that in all the canon fiction set in the 41st millenium era (in the universe's present) is that if the Imperium is involved then they will end up winning which means that all of the huge and vastly convoluted plans that we get to hear about are pretty much doomed to failure by narrative convention. This normally happens by the space marines (or whoever) headbutting their way out of the trap even against absurd odds that even by the universes own standards should be impossible. Thus, Tzeentch and his followers never get to show off just how good their schemes are. They are definitely supposed to be magnificent bastards, particularly with Magnus following his own weird agendas rather than the general chaos 'go and murder stuff' manifesto. Sadly, we only ever get to see them fail and that takes some of the punch away.
Then there are the Thousand Sons Legion, whose meticulous planning runs for centuries, every detail mapped out, completely flawless, until the Space Wolves show up, kick their teeth in, then laugh at all the effort Tzeentch put into those plans- unless of course Tzeentch just enjoys watching Magnus the Red and co suffer. The Space Wolves, a whole army of Spanners In The Works, they keep the Thousand Sons from ever becoming 'proper' Magnificent Bastards.
The TRUE Magnificent Bastard regiment of Warhammer 40000 is, as said above, the Alpha Legion. Contrary to the Thousand Sons' meticulous planning over the years (which gets screwed up anyway), Alpha Legionnaires are trained to think for themselves and to improvise in the heat of battle. Their combat doctrines include multiple strikes at various enemy weak points at the same time, using cultist regiments that are well-trained instead of mere cannon fodder, and fighting dirty when push comes to shove. In an event following Horus Heresy, the Ultramarines clashed with the Alpha Legion and managed to catch them off-guard by deploying their best strike force directly to the Alpha Legion's command center. Despite managing to destroy the Alpha Legion's central command which included their Primarch, the Alpha Legion managed to keep their cool and coordination under the circumstances. Using various tactics such as ambush, traps and False Flag Operation, they managed to almost completely obliterate the remaining Ultramarine force, forcing the Ultramarines to retreat hastily and their Primarch remarking that he "has no interest in a righteous war against such a dishonorable foe"
Their magnificent bastardy is enhanced by the fact that that story may well not be true - the only source for it is an Inquisitor who was later revealed to be an Alpha Legion spy.
The latest Dark Eldar codex is full of them:
Asdrubael Vect, overlord of the Dark Eldar city of Comorragh. He actually engineered a Space Marine inavasion of said city when he was a lowly kabal leader to remove the more powerful rival kabals. Since his ascension, he has always been two steps ahead of everyone else in the insanely byzantine politics of the place for over seven millenia. He has risen from seducing noblewomen into assassinating their annoying parents to delivering actual black holes in gift boxes to retainers that were barely starting to consider challenging him.
Lady Aurelia Malys, Archon of the Kabal of the Poisoned Tongue is certainly one of the queens of Magnificent Bitch-dom. She started out as a courtesan of Asdrubael Vect, but when he got tired of her, he banished her. She took her followers with her, and journeyed into the Webway, seeking fortune. She bumped into a god-like trickster being (heavily implied to be the Laughing God) and beat it in a game of wits. As a reward, she got its sword and its heart (she then cut out her own heart and replaced it with the new one). She is now carving a (perfect) figure in society and, if Vect ever falls, she'll be the one holding the knife. Oh, and she stole a heavily guarded STC machine from the Imperium just because she could.
Prince Sliscus, the arch-pirate. He stole three Archons' flagships just to show off, and defeated them when they tried to get them back. His pirate fleet is one of the largest in the galaxy, and he is a Memetic Badass in Comorragh - a city of the most evil and twisted murderers possible. Lady Malys, herself a Magnificent Bitch, described him as "amoral, despicable, and impeccably dressed."
One of the basic requirements to be a Dark Eldar Archon is to be a mild Magnificent Bastard, as the entire race as a whole is plagued with a serious case of Chronic Backstabbing Disorder. Keeping three or four steps ahead of your own servants is apparently as common as breathing for many archons.
Also, the C'Tan Deceiver. He works on the same level as Tzeentch, playing the other races of the galaxy, including the Necrons themselves, against each other for his own benefit.
On the subject of divine masters of the various Gambit tropes, there's Cegorach, the Laughing God. He was the only Eldar god to fully survive the birth of Slaanesh (Isha was captured by Chaos, and Khaine was killed but lives on in some sense through his avatars), and remains the mastermind behind many of the Eldar's most complicated and successful schemes. Arguably fits into the Guile Hero trope as well, but many a being that qualifies as a "hero" by 40k standards would be hardly better than a villain in most other settings.
Before the overhaul of Necron fluff that came with their 5th-6th edition codex (and the in-universe nerf of the C'tan), there were a number of in-universe hints that the Deceiver and the Laughing God are one and the same (in fact there are hints dropped all over the place that most deity beings are C'tan in disguise, such as hints that the Omnissiah is actually the Void Dragon). Should that turn out to be the case that would elevate the Deciever into previously unheard levels of magnificant bastardry beyond normal human comprehension.
One interpretation of Cypher would mark him as this. On the surface he seems to be an enemy of the Imperium. Everything Cypher does basically goes off without a hitch, then he leaves right after drawing Imperial forces hunting him to a group of enemies Cypher was supposed to be "helping." Cypher being in this trope does depend highly on his motivations though.
It doesn't really matter what interpretation you like, Cypher definitely has the magnificent bastard base stats. He has his own secret shadowy goal, he's smart enough to have wandered the cosmos for eons furthering that agenda without being caught, he's manipulative enough to con anyone around him into murder if he wants, and charismatic enough to worm his way into various factions around the galaxy, so he definitely fits the trope.
And one of the greatest Magnificent Bastards of the Warhammer 40,000 and Horus Heresy universe is Erebus. He corrupted not one but TWO Primarchs, both his own, Lorgar, and Horus; convinced Horus that the Emperor was his enemy by endearing himself to the Luna Wolves Legion and was able to get Horus to trust him over his brother Magnus the Red; he helped plan the Istvaan Massacre and taught Horus everything he knows of Chaos; During the battle of Calth he used his own forces as a distraction to cast a powerful ritual that made warp travel near impossible throughout the Imperium and prevented communication, so that Horus's treachery would remain secret for longer and the Loyalist forces could not strategize with each other long-range. If it weren't for Erebus the Horus Heresy would never have happened, he is responsible for the crapsack state of the 40k galaxy. And to make him even more magnificent he survives the Heresy and goes on to be one of the two most powerful figures in the Word Bearers legion, possibly one of the most powerful warriors alive, and is still a Magnificent Bastard; he and Kor Phaeron using the entire Legion in a civil war as part of a game between them that in Erebus's own words "means nothing,", a war which his side won, and possibly planning Abaddon the Despoiler's downfall as his next move. Truly a more Magnificent Bastard has never lived, one that ruined a galaxy just to gain power.
Khazrak the One-eye, a beastmen leader from Warhammer Fantasy. A ruthlessly efficient beastmen who uses simple yet effective ambushing tactics. He has a rather one-sided Friendly Enemy relationship with the count of Middelland and really believes in an eye for an eye. Even though the count sends knights, soldiers and mercenaries his way, and has put a price of a whopping 10,000 gold pieces on his head, Khazrak keeps one-upping everyone he meets (and even if he somehow gets caught, he will escape and exact revenge on whoever caught him). The fact that he's from a race that's not too good when it comes to smarts is just icing on the cake.
Legend of the Five Rings has the Scorpion Clan, which basically trains every single member from birth to try to live up to this trope, with a frightening degree of success. However, while the Scorpion Clan might specialize in it (and get the most attention for it), just about every major organization in the setting has a good half-dozen or so examples that qualify. Of course, there's also the Kolat, who tend to be as magnificently bastardy as the Scorpion Clan but for entirely different reasons. That is, until the Scorpion Clan found the Kolat's secret hideout and, in a surprisingly unsubtle but extremely effective maneuver, sent in a crack team of killers to wipe out as many Kolat as possible and stole the Kolat's magic scrying device that they needed to remain the super-secret all-knowing conspiracy, thus giving the Scorpion Clan a monopoly on Magnificient Bastardry within the Empire.
Mostly because one of the most common tactics for a good Scorpion is to pretend to be a Defector from Decadence or some similar type - basically convincing their marks that they're not like the rest of the OBVIOUSLY untrustworthy Scorpion Clan, they're different, honest! Also, despite being Magnificent Bastards, most have as the goal of their schemes 1 ) Personal power and glory; 2 ) The survival of the Scorpion Clan; and 3 ) The survival of the Empire. They may be nasty sons of guns, but they're still (mostly) loyal.
Also, the ones who aren't pretending to be Defector from Decadence instead just master Batman Gambits, by being trustworthy when you expect them to be untrustworthy. The Scorpion book is basically a guide to how to follow this trope.
Duke Rowan Darkwood, factol of the Fated in Planescape. Where to begin? His backstory is that, after retiring from a successful career in adventuring, he successfully out-cheated a devil in a card game for the souls of his family, then spent the next decade being tortured in the pits of Hell, before being released on the grounds that he was too tough to be fun torturing anymore. Upon arrival in Sigil, he took over one of the city's most powerful factions in under a month, persuaded the leader of the Mercykillers faction to team up with him, and immediately began plotting to conquer the entire city. After setting off the Faction War and eventually being defeated, he became one of only three known people in recorded history to escape from one of the Lady of Pain'sMazes.
Faction War, however, makes you wonder if Darkwood managed to escaped the Mazes only because the Lady of Pain wanted him to in order to create one of the biggest Time Loops in D&D history —- warping him 500 years in the past to become Gifad and end the Faction War he started, and then ages in the past when he naturally fails...into the very wizard who would craft the Sigil Spell that would prompt Darkwood to start the Faction War in the first place! As is a recurring theme in Planescape, it goes to show him that he can't fight fate...
Nicol Bolas of Magic: The Gathering is slowly becoming one. The oldest being in the multiverse, he successfully manipulated other planeswalkers into sacrificing themselves to fix universes, as well as having deceived Sarkhan Vol into becoming his stooge and awaken the Eldrazi for a yet-to-be-revealed scheme. He's such a Magnificent Bastard that he bullied, coaxed, or conned the designers to give him a card that, for raw power (though probably not game-breaking effectiveness like Jace), is probably stronger than any other Planeswalker yet printed.
Did we put some juice into Bolas's design? Yes. Will this be cause for some complaints? Yes, it will. "But +3 loyalty every turn, and starting at 5, make him way too hard to kill." Yeah, too bad. It's Nicol Bolas. "But blue, black, and red aren't supposed to destroy enchantments." Yeah, too bad. It's Nicol Bolas. "But a Control Magic every turn is too much card advantage, even for eight mana. And even if you say he's not supposed to create immediate concessions, his ultimate is basically game over." Yeah, too bad. Deal with it, folks, it's Nicol Bolas!
In one article, written in character, Nicol Bolas actively encourage players to cheat whenever possible, saying that it wasn't against the rules as long as you don't get caught. Of course a bastard as magnificent as he could never be caught.
Actually, Bolas points out that cheating, while a path to assured victory, is also the least reliable. A bastard as magnificent as he can screw you over perfectly fine without even bending the rules.
Niv-Mizzet of Ravnica also fits this trope, along with Ral Zarek to a lesser extent.
Cyric in Forgotten Realms. Pretends to hold the Idiot Ball for almost ten years, but ends up getting exactly what he wanted and manipulates almost the entire pantheon of Greater Gods and ends the love of an Established Couple. He eventually KILLS one of the most powerful goddesses in the entire Realms through some Xanatos Speed Chess between he and another Greater Evil God. He also convinces an Eldritch Abomination to work for him and seals his loyalty so much that the thing is still loyal to him to this day. This guy puts the "bastard" in Magnificent Bastard.
His losing the Realm of the Dead was apparently intentional. Cyric never intended to rule over death. He enjoyed chaos and tricks far too much to waste time on judging the damned. It's possible Cyric set up the whole thing so he would end up losing the Realm of the Dead and be able to take his true place in Pandemonium, where he is far, FAR more powerful than he was in the Realm of the Dead. Cyric is also quite capable of playing Xanatos Speed Chess, as evidenced in the novels where he DOES ALL OF THE ABOVE MENTIONED THINGS! If Cyric isn't a magnificent bastard, no one is. Oh, and he also tricked Tyr, the FREAKIN GOD OF JUSTICE (the Big Good) into murdering another good god out of jealousy that Cyric managed to stir up using his lies and tricks. No wonder he is currently in chains somewhere. But it took three greater gods just to put him in chains in the first place. Methinks Cyric won't be in those chains for long.
The New World of Darkness sourcebook Mirrors includes the Merit "Magnificent Bastard", which means that a character suffers from no situational penalties for attempts to Sway others (i.e. no matter how guarded a person is due to warning, previous betrayal, or catching the character in a compromising position, the character will always find a way to get in with them).
Brem Marst, after having an epiphany whereby he realised that even the mightiest supernatural beings were reliant on trade and finance one way or another, and that an appropriately enterprising group could use this need to secure themselves and profit immensely, conned every last penny out of a bunch of Cargo Cults, used the money to buy into a network of merchants and manufacturers, and had them take advantage of local political instability to found the Guild and establish the guiding principles that made it the second most powerful organisation in the world. Even after dying, Marst was committed to his own fortunes; he leveraged his connections in the Guild (particularly the worship they could offer him in exchange for protection and their information networks) into becoming the fastest rising anacreon in the history of the Timeless Order of Manacle and Coin. Not bad for a mortal.
The entire Fiend Caste of Infernals either are this, or would be very good at it if they tried. Mainly because they get Charms from the Ebon Dragon, who is quite literally the biggest backstabbing son of a bitch in the setting.