A few chapters later, Fuyutsuki invokes the trope by name when Gendo returns to power.
Loki, the Big Bad of My Little Avengers, who has the rather telling nickname of "The Magnificent". True, he probably gave himself the title as a bit of ego stroking, but he definitely lives up to it. At the climax of the story, he reveals that the entire plot up to that point was a Gambit Roulette: by removing Celestia as a potential threat via depowering her, he causes a Mass Empowering Event that lays the potential for the world ruled by magic he's long envisioned, and more importantly insures that Big Mac will end up with teammates — teammates that Loki can threaten in order to force Mac to surrender Thor's powers to him. And it works perfectly, with him only being defeated afterwards due to Pinkie being a bigger Spanner in the Works than anticipated. He also shows that he anticipated Trixie's betrayal and deals with it effortlessly. Hell, he even manages to die with style — as he lays dying from his own reflected spell, he revels in the fact that the magic released by his death will mutate all of Equestria, creating the world ruled by magic he's always wanted, then dies with a smile.
The Naruto fanfic "Yakuza" makes one out of Hinata, of all people. Let me break it down for you: the Rookie 9, Team Gai, and the Sand Siblings all play a game of Yakuza, with Lee and Hinata as the yakuza. They both manipulated everyone into killing the Genin they didn't kill themselves, and at the end, Hinata betrayed Lee, causing him to kill himself in confusion, and refused to kill Naruto, leaving them the sole survivors, with Naruto taking her for ramen to celebrate.
Erasmius Servius from the Elder Scrolls fic 434: The Last Year of the Third Era definitely qualifies. He manipulates every one of his enemies with relative ease, and even when Plan A of his bid to become emperor fails, he doesn't panic at all; he simply falls back on his other plan: trapping theDaedric Lord Molag Bal and using him to power a thousand-foot tall war machine. And true to the trope, when he wakes up in the afterlife and finds out he's likely going to have his soul torn apart by the Daedra for daring to outsmart them, he doesn't do much besides accept defeat calmly and enjoy what little solitude he has left before eternal torment.
In The Wizard in the Shadows, or rather, its sequel, Draco Malfoy is showing signs of this, after casually pulling a Sherlock Scan on some of the most dangerous people in existence while drinking tea.
Draco: Potter, when people expect to see a pretty face, that is all they see.
Lately, this has started to be seen with Albus Dumbledore in many Harry Potter fics. We'd list them, but there are too many to list.
The Uplifted series features a few examples of this trope. Erwin Rommel is the trope namer and best example in the series, but it is really Admiral Halid Zorah who takes the cake. A brilliant diplomat and negotiator, he is responsible for organizing the coup against the Nazis. Hanala Jarva seems to be one in training, as she is brilliantly manipulative and cunning, despite her youth and inexperience which shows. John Hoch, from what we've seen in the interludes is certainly one, and Joachim Hoch seems to have the potential, at least in his later years. Not surprising as John and Joachim are actually the ancestors of the Illusive Man.
Ivana M. Kiljoy from the Rescue Rangers epic fanfic Rhyme And Reason is this in spades. Without spoiling too much, she manages to kidnap Monty, Dale, Gadget and Zipper and subject them to tormenting and deadly challenges, while at the same time, making Chip travel all over the city in order to find rhyming hints to save them. She demonstrates an incredible intellect and genre savviness, a deep knowledge of the Rangers' personal histories (almost all of her clues and trials relate to a past case in some way), and an utter disregard for both human and animal life.
Princess Platinum, due to the throne of the Kingdom of Unicorns being effectively a figurehead by the time she takes it, was forced to spend her entire reign manipulating her entire Deadly Decadent Court in order to get things done the way she wanted. Then, after the Warming, she realized that the nobles were risking the newfound peace between the tribe, so she had most of them killed — something that was both viewed in universe as a Kick the Son of a Bitch moment and had had the groundwork laid years in advance — before stepping down from the throne for the newly formed Equestria. And then she kills herself (making it look like an accident, of course) in order to end the royal line and finally break what power the nobles had left.
Though you'd never know it from the main narrative, side stories deconstruct this trope, showing how someone who thinks in such detailed plans would have trouble seeing the line between casual interaction and the shuffling of chess pieces.
General Wind Whistler, who spent her whole career as a Chief-Of-Staff standing up to Commander Sullamander and denying as many of her outrageous decrees as possible, and managed to survive her defiance. Then, on top of that, she manipulates several of her fellow Generals into staging a coup against Sullamander — simultaneous to a Gladiator Revolt led by her lover Hurricane — that succeeds in bringing her down though it costs Wind Whistler her life as well.
Lady Cripps the Pink, who's such a tactical genius that during the Lake Trot Crisis, she not only beats the Celestine Junta — the greatest military force in the world — but her forces suffer only one casualty... who dies from choking on a sandwich.
In Child of the Storm an Avengers/Harry Potter crossover, Loki indicates that though he is good these days, he is still one of these and a Chess Master to boot, as well as being all the more terrifying for being sane, as he is no longer burdened by Smug Snake tendencies. He also tells fellow Magnificent Bastard Dumbledore that he knows his schemes - which he demonstrates through a chess metaphor, and he is willing to tolerate them, even assist them, but if they hurt his brother or his nephew (Harry) - and he will know, because he will be watching - then he will have nowhere to hide.
Loki also very publicly offers several wizard children who lost their parents in New York the chance to kill him, with it being very clear that he knows that they could never do it.
Lord Silvertongue comes up with a plan that will further his goals. If that plan fails, he twists the failure so precisely that it becomes a success somehow as part of a new plan. His manipulation, charisma, and silver tongue allow him to get the better of every creature he interacts, including Nihila, a goddess that exemplifies evil traits, including deception.
From Young Justice Darkness Falls we have both Vandal Savage and Lex Luthor. While Savage is more diplomatic than magnificent, he still organizes the attack on the watchtower, takes control of war world, and even plots to have all earth converted into One World Order like a boss. Luthor is much more of a bastard, and perhaps even more so when he betrays the operations of the light in order to weaken their positions so that when Vandal stepped over the line, he might become leader of the light. He also worked in plain sight as a UN representative, almost taking total political control of the league, and still managing to cover his tracks when his own bodyguard helps one of Darkseid's pawns escape. Luthor is just in control of his actions and influences for most of the fic.