The Snake in Above Ground is a prime example, particularly because he can use magic to enslave others into doing his will.
Regine in Addergoole - the school, and the students, exist to fulfill her plans.
Bavandersloth in Angel of Death pulled a pretty impressive gambit when he set fire to a police station to free Cody and kill detective Williams.
He's since been revealed to be planning something much bigger, though little is known about his new plan, save that it's objective is to turn the partial breaking of The Masquerade to the community of liches' advantage.
Dreamscape: Melinda's plan in breaking her seal involves parallel universes and using anotherSealed Evil in a Can to manipulate her former apprentice into nearly breaking that evil out! It only went awry because of an "I Know You're in There Somewhere" Fight. In "Confronting the Dark", Melissa even lists cunning, manipulation, and trickery as Melinda's biggest qualities.
In The Gamer's Alliance, quite a few villains such as the Master and Iblis end up being quite good at manipulating events into their liking.
Andross qualifies as this in Gaming All Stars: The Ultimate Crossover and Remastered. While the remainder of the villains capture other characters as trophies and attempt to establish themselves at the top of the barrel, this character waits in outer space, planning for one of those worthless baddies to force the moon to plummet toward the Earth and allow him to unleash titans that had been contained inside of it. While doing so, he makes arrangements with Polygon Man to lure the main antagonist/s (Eggman, G-Man, and Cortex in The Ultimate Crossover, Radec in Remastered) by having PM claim that hell provide them a boost of power to help them kill the heroes if they meet within inside the moon. Once Polygon Man takes care of them/him, Andross finally reveals himself and manages to kill nearly every hero standing against him. However, his plan comes undone when Master and Crazy Hand break free from Polygon Man's hypnosis, summoning a subspace bomb to destroy the moon and undo the chaos Andross had orchestrated.
Hoody of Marble Hornets is this of season 2 and 3 of the series. Introduced in Entry 41 after retrieving Jay's camera after the latter was attacked by The Operator. He stayed around, making sure certain things happened.
Technically, whoever was in charge of totheark during season one could be this as well, telling Jay to go to certain places, ie Brian's house the second time, and also the red tower, where Seth's fate was revealed.
Nick Fury, Charles Xavier Sr., Forge, Tzigone, Vengeance and many others from Marvels RPG.
Jenna Darabond herself was pretty manipulative, as the start of season 3 reveals she was behind everything of the last 2 seasons.
A downplayed version gets subverted in Noob Season 2 finale. Two of the protagonists arrive at the only place where they can destroy an item that can put them in big trouble with the game authorities if discovered in their possession. Their former Guild Master, who wants them kicked out of the game, suddenly shows up, claims to have requested one of the MMORPG's Game Masters and plans to fight them while waiting for its arrival. When asked if he had been planning this all along, the former Guild Master replies that had just been spying on them and had come up with the plan on the spot.
The Architect (no, not that one) is hinted at being this in Shadowhunter Peril. However, he tends to go against the grain of the usual Chessmaster, as he is a genuine hero...he's just hiding a lot. He's actually a dimension hopper who has visited multiple universes and seen how events will play out depending on the choices made, so he's just really knowledgeable because of his experience.
To Welcome Oblivion has Noah T. Trepaly, who spent the entire story letting Dr. Lilith Madison do all the heavy work while he remained in the background watching. As soon as it was convenient, he subdued Madison and started using his powers to cause chaos around the world, with hardly anyone left to oppose him thanks to Madison's work.