And Then There Were None: Judge Lawrence John Wargrave, aka U. N. Owen manages to craft the ultimate Locked Room Mystery and only his desire that someone appreciate his genius allowed the mystery to be solved. Wargrave, deep down, is an admitted sadist with a bizarre sense of justice and only enacts his cruelties beyond the guilty and evil. When he realizes he is fatally ill, Wargrave has nine unrepentant criminals lured to an island with him where he begins murdering them, and avoids suspicion by luring a doctor there into helping him to fake his own death, then murdering said doctor as well. Wargrave proceeds to eliminate his other victims, pressing the final main character who had manipulated a child in her care to his death into suicide. Wargrave ends his plan by committing suicide in such a way that obscures the way he died, with only a written confession in a bottle thrown into a sea revealing the truth.
The Elenium: Martel is a renegade Pandion Knight, Dragon-in-Chief to Azash, archenemy of protagonist Sparhawk, and the primary planner behind everything the villains do. Having procured the poison that Primate Annias needed to incapacitate Queen Ehlana, Martel moves about Eosia, stirring up trouble in Rendor and Lamorkand in an effort to draw the Church Knights out of Chyrellos and make it easier for Annias to gain the Archprelacy by way of intimidation. When Sparhawk and his companions foil these plans and restore Ehlana to health, Martel convinces the Rendors to invade Arcium, then attacks Chyrellos with his own private army of mercenaries. Robbed of victory by way of divine intervention when the Child-Goddess Aphrael steps in and leads King Wargun's army to Chyrellos, Martel lures Sparhawk to Zemoch, so that Azash can deal with him, and steal the Bhelliom—the entire plot of the series, from the poisoning of Ehlana onward being revealed as part of a scheme to force Sparhawk to uncover Bhelliom and then take it from him. Out for his own profit first and foremost, Martel used Annias, Zemoch Emperor Otha, and even Azash, as means to his ends, hijacking all of their plans in order gain revenge on Sparhawk and empower himself.
Gentleman Bastard: Luciano Anatolius, alias the Grey King, alias Capa Raza, used Locke Lamora and the other Gentleman Bastards as disposable pawns in his campaign against Capa Barsavi and the Camorri nobility, forcing Locke to impersonate him so that he might fake his own death, and then killing off most of the team with ease. With twenty-two years to plan out his revenge on Barsavi and the nobles for the death of his family, Anatolius leaves few details unattended to, killing off Barsavi's gang bosses and inserting his own men into leadership positions, hiding his Co-Dragons among Barsavi's personal bodyguard, and hypnotizing the chief of the Secret Police into bringing his hidden Wraithstone weapons into the Duke's ball. Successful at taking over the Barsavi organization and killing off Barsavi's entire family in the process, the newly minted Capa Raza comes within a hairsbreadth of taking out the whole of the Camorri nobility, before Locke and Jean manage to halt his rampage.
Amy Elliot Dunne in Gillian Flynn's Gone Girl finds out her husband Nick is having an affair, so on their fifth anniversary she goes into hiding, leaving behind a series of clues for their traditional anniversary "treasure hunt" specifically so he'll inadvertently follow them to evidence and locations that incriminate him; she also spends months forging a diary full of completely invented incidents of Domestic Abuse to make it seem like she was afraid of him killing her, and orders hundreds of thousands of dollars worth of expensive stuff in his name, even going so far as to take his fingerprints and smear them on all the merchandise. But it doesn't stop there- when she decides against letting him take the fall, she kills the Dogged Nice Guy school friend she'd been hiding with and tells the police she escaped after he kidnapped her.
Captain Kennit from the Liveship Traders trilogy. He is a handsome pirate captain, sharpwitted, crazily manipulative and achieves being loved by almost anyone revolving around him, including smart characters such as Wintrow or Etta. And there's almost anything he won't do to become the King of Pirates.
Neuropath: Neil Cassidy is a charismatic neurologist and former college roommate of protagonist Thomas Bible utterly obsessed with Thomas' old philosophy of "the Argument." To convince Thomas to adopt the Argument's principles again, Neil executes a long, complex mind game through a series of murders and manipulation while ruthlessly rooting out any loose ends. Suave and eloquent enough to make Thomas continually question his own reality, Neil reveals he made Thomas' partner in the case to have been a mole of his own making; that Thomas' own beloved son Frankie is in fact Neil's; and uses a device he uses to rewire parts of Thomas' mind to show to him in perfect detail the fundamentals of the Argument, having previously used the device to erase all forms of human emotion and weakness from his mind to perfectly devote himself to his master plan and nothing else without the hindrances of love and guilt.
Second Apocalypse: Anasurimbur Kellhus is a powerful Dunyain monk who implants himself in the holy War in opposition to the monstrous Consult. Scheming and manipulating all in his path, Kellhus engineers his own death and supposed rebirth to be seen as a great savior, eventually rising to utterly dominate the Three Seas as the powerful Aspect Emperor and prepare the world to fight the Consult. Manipulating almost everyone he meets, Kellhus heads the Great Ordeal, a grand crusade to completely break the Consult and even allies with a deadly God to destroy their conspiracy for good, vowing to conquer even damnation itself.
Six of Crows: Villain Protagonist Kaz Brekker is a gangster, conman, bank robber, blackmailer, and all around criminal prodigy who uses his extensive knowledge of Ketterdam's secrets to shame richer and more respected men and women into helping him with his schemes. Whether its bluffing gunmen into backing down with fictitious threats against their families, arranging breakouts from the two most heavily guarded prisons in Ketterdam and Fjerda respectively, or running a con on the entire government of Ketterdam that drags in King Nikolai of Ravka as coconspirator, Kaz proves to Pekka Rollins, Jan Van Eck, and all his other competitors that he is the true kingpin of Ketterdam.
Tolkien's Legendarium: The Silmarillion and The Children of Húrin bring us Glaurung, Father of Dragons, and Tolkein's most competent antagonist. Serving as Melkor's greatest field marshal, Glaurung broke the siege of Angband, and crushed the armies of Elves, Dwarves, and Men at the Fifth Battle, ushering in an era of dominance for Melkor's forces all across Middle-Earth. Chosen as the instrument of Melkor's curse against the Children of Hurin, Glaurung tricked Turin Turambar into allowing the city of Nargothrond to fall, then hypnotized Turin's sister Nienor into falling in love with Turin and becoming pregnant with his child. Slain by Turin in an ambush, Glaurung used his final breath to reveal the extent of his manipulations of Turin and Nienor both, resulting in their suicides as they contemplated the horror of what they had done. Victorious in death, Glaurung completed every part of his mission from Melkor, and brought complete ruination to the family of Hurin.
The Three Musketeers: Cardinal Armand Richelieu is the most powerful man in France, and the ruler behind the throne. Seeking the betterment of France as a nation under his guiding iron hand, Richelieu schemes to strengthen the monarchy and to also start a war with England to further check Spain and Austria. In order to disgrace his rival, Queen Anne, Richelieu convinces the king to throw a party and request Anne wear diamond studs he gave her as a gift, well aware Anne has given them to her lover, the Duke of Buckingham, which will discredit Anne and begin a war with England. When the Musketeers recover the diamonds in time, Richelieu accepts it with grace, later deciding to have Buckingham assassinated and presenting the wicked Milady de Winter with a letter excusing her from all acts she commits in service to France. When Milady is executed by the Musketeers, young hero D'Artagnan thinks to save himself by presenting Richelieu with the same letter, only for Richelieu to display his own power by tearing it up. Impressed by D'Artagnan, however, Richelieu accepts him as a Worthy Opponent and a boon to France, writing him an officer's commission to the Musketeers before focusing on his next schemes to ever better France as a nation.
The evil queen protagonist of the short story A Woman's Work by Tanya Huff qualifies. She has a plan for everything that could happen ... for example, when an assassin's horse looks at her with intelligent eyes, she shoots it, and says "Horses don't have intelligent eyes", implying that it was not a mere horse, but the enemy's backup plan.