In Freefall, Dr. Bowman says that another character keeps losing to him because he can't see five moves ahead. The "several moves ahead" matter applies to the rest of Bowman's plans, since every last hang-up, problem and unforeseen consequence his project might have ran into had already been covered before anyone even considered the possibility it might come up, and even end up covering the problems he couldn't have thought of (like Kornada's scheme, foiled by one of his creations).
In Homestuck, Doc Scratch and Vriska are implied to play long-distance games of a variation on chess using cubic and spherical boards. Doc Scratch, who has near-omniscience, playfully reminds Vriska of her consistent failure to defeat him, even when he tells her his next 100 moves in advance. Even when she cheats using her own omniscient oracle, of which he is unaware. Paralleled in his later schemes, where he is able to manipulate several of the cast into doing exactly what he wants, despite being completely honest about his motives as a Card-Carrying Villain who exists solely to bring about the rise of an Indestructible Demon.
The chess theme in Homestuck also persists in terms of the game they play— a checkered battlefield where white fights black, and inevitably loses. However, manipulating this game of chess is unnecessary, and ultimately futile, unless someone decides to smash the board.
In addition to the chess motifs, Doc Scratch's overall theme (and the theme of Lord English and the Felt in general) is of another strategic game: American eight-ball pool.
Dirk is rapidly becoming one of these, which fits with his puppet theme. He assured Jane early on that he would be "the one pulling the strings here," and hehasyettodisappoint.
Ultimately subverted, as Dirk eventually points out that the Auto-Responder was doing much of the planning during [s] Dirk: Synchronize and [s] Dirk: Unite, to the point that Dirk only realized the full extent of everything afterwords. Granted, the Auto-responder is a hyper-intelligent AI with a personality copied from his thirteen year old self, so in a way it still fits.
Terezi is also this. As a Seer of Mind, she has a comprehensive understanding of the effects that decisions will have. This means that she is incredibly good at manipulating and tricking people, from physical gods to reality warpers. Vriska is not happy about this.
Billy Thatcher from morphE is a chess grandmaster on his way to the World Chess Championship. Then he awakens as a Obrimos mage. He's arrogant enough to think that his chess expertise can translate in to real world situations.
In Erfworld, Charlie manages to manipulate circumstances - WARS - so that he will * always* end up on top. And he gets paid to do it.
"When you're working for Charlescomm, you'll learn. We prefer to play games that don't even contain a losing outcome. You see?" "Yeah, yeah... you turned it into a no-lose situation by rejoining him." "Oh no! No, I got paid to turn it into a no-lose situation. :)"
Skerry from Fite!, who uses a more generic gameboard rather than a chessboard. And really, he's just a doctor trying to wake Lucco from his coma.
In spite of her misleading middle name, Pandora Chaos Raven of El Goonish Shive is the epitome of this trope. As an Immortal who has lived for millenia, her joy comes from notknowing what will happen next. Despite this, her actions are cold and calculated, and she pulls the strings of everyone she meets. Her tendency to stay behind the scenes is not due to any sort of weakness (Immortals possess near god-like power when on the Spirit Plane, and can use magic without being detected), but rather because the other Immortals get seriously pissed off if one does anything more than empower or guide people on the Physical Plane. That, and doing everything herself would just be boring to her.
In Grim Tales from Down Below, Grimm's journal reveals that Mandy, had planned a series of events to convince Grimm to give Billy his powers for a day. Then when done, she convinces him to give his powers to her to make it fair. Later, while snooping through her room, Grimm finds plans for initiating the 9/11 attacks on the World Trade Centers and Pentagon. Her plans also included the United State's response: Operation Iraqi Freedom BEFORE it happened.
Sonorous Aria, from Keychain of Creation, is stated to be one. Most of her chessmastery is offscreen, so far.
Marena: Everything she does is layer on layer of sheer deviousness. Aria: Now, a feast! Lavish meals and fine drinks for everyone! Then: Party games! Marena: She's up to nine layers already. Aria: Extra drinks for the handsome bearded fellow in the corner! Marena: ...twelve.
MAG-ISA — We have an unnamed reptoid (or demon) villain who seems to be calm even though the mind-control experiment has seemingly failed. Is it because... he's got another plan and its all a diversion?
Yukizane Masamune from No Need for Bushido, is also one of the few 'good' Chessmasters. He starts out in the series as being questioned on his leadership capacity due to his silliness and focus on playing Go (the Japanese answer to chess) as opposed to grunting manly and flexing. He, however manages to shine several times and manages to deceive a ninja.
In The Order of the Stick, Lord Shojo provides an interesting example of the non-villainous chessmaster, ruling Azure City and the Sapphire Guard with the aid of a series of deceptions.
And Nale, especially at the Cliffport arc, gives us the more traditional villainous one.
And in comic 830, Red Cloak is revealed to be one who's manipulating Xykon.
Posey from The Sanity Circus can guide and manipulate people and also outpredict them with reliable frequency. She knows even that steering Attley and co. to find Nimbus Owens would lead to them visiting Dr. King, which would prompt King to shoot Attley and let her catch both Attley and Nimbus together.
The nigh-omnipotent AI Petey from Schlock Mercenary doesn't have a chessboard (although one strip features him playing checkers). One of his most complicated capers involved:
Convincing all A.I.s to join him and mutiny against their captains, forming an instant galactic power for the purposes of combating an enormous threat to said galaxy.
Refused to pay the main characters for their ship, which blew up while carrying out his orders, then bribed a few councilmen to get them a new one anyway (at the expense of most of their savings). While keeping it all under the table in an attempt to force the company's AI to act as his spy.
Manipulated the government into hiring the (now short-on-cash) main characters to destroy a reality-TV network.
When the main characters got in trouble carrying out his gig, bailed them out with blackmail (after playing with their heads) and turned it into his own form of leverage on them.
The new ship AI 'Tag" finished to discover his true plan but only revealed the Social Engineering from the government to let Petey know that he know he is the one the manipulated them into it. (ironically the only clue that permit to the AI "Tag" to come to this conclusion was the analysis that the UNS government leadership is too short-sighted to plan that much.
Skin Horse: After literally years of mystery, Ira Rosenkrantz is revealed to be Mr. Green in this brilliant (if slightly long-winded) reveal.
Dr. Schlock seems like a harmless coward and Chew Toy with some minor Manipulative Bastard tendencies for a long time until Hereti-Corp finally pushes him too far by becoming a never-ending threat to the one thing he cares the most about (his own well-being). At this point, pushed into a corner, he feels forced to execute a plot to take over H-C and become the new Diabolical Mastermind behind its schemes, taking everyone by surprise and becoming the closest active character to a Big Bad in the comic.
The Big Bad of We Are The Wyrecats practically lives and breathes this, somehow managing to manipulate the entire human race while also stringing along a team of kids using Powered Armor that should be strong enough to flatten him to a wafer-thin pulp, if it weren't for the fact that he's backed them into a corner to the point that they either do his bidding through gritted teeth or else go entirely off the grid just to get away from him.