In All Fall Down, AIQ Squared becomes this, hatching an elaborate plot to try and kill Siphon, using Phylum and Pronto as his less-than-willing pawns.
The Avengers villain Immortus was always a Chessmaster in a big way, but in the Avengers Forever series it turned out he was a Chessmaster on a far greater scale than anyone had imagined, he had manipulated virtually every event in the history of the Avengers simply to prevent the human race from becoming dangerous enough that the malevolent Time Keepers would wipe them out to preserve their own existence.
Batman villain The Riddler is an accomplished chessmaster, notably for smooth sway over the media, especially post-reformation (a quality of Villain with Good Publicity), and for his previous yet strategically subtle maneuverings of other well-known manipulators and dangerous personas.
In Hush: The Riddler discovers Batman's secret identity and manipulates Bat's oldest friend and his old mechanic, Poison Ivy (who in turn uses Catwoman and SUPERMAN), Killer Croc, Harley Quinn, Clayface, Scarecrow, Ra's Al Ghul. Even the Joker was talked into going along with his scheme. However, Batman ensures his confidentiality when he exploits the Riddler's compulsion: he can't expose Batman because it would be like giving away the answer to a riddle.
Two-Face can also be a Chess Master, usually having two plans in motion at once, one often entirely different (but also in some way linked) to the other.
Ironically, this could have backfired on him when he engineered his greatest scheme in Knightfall, springing the entire Rogues Gallery from Arkham Asylum knowing that Batman would physically exhaust himself trying to recapture them all, leaving him vulnerable to the above-mentioned back-breaking. A few of the villains manage to figure out they're being manipulated - and one of them, the Mad Hatter, enlists the help of Film Freak (by brainwashing him) into helping investigate who's behind the breakout. Film Freak discovers Bane and attempts to assassinate him, only to be beaten to death at Bane's own hands - thus, ironically, leaving Batman with one less problem to handle.
In Red Robin Tim proves himself to be taking after his adoptive father in stride when he sets up his own information network and a "hit list" arranged so that the capture of one criminal will lead to the arrests of about fifteen others, that can easily be tweaked and modified to the point that he can free a couple of the villains on it without it affecting the overall plan.
Batman himself. He is the namesake of the Batman Gambit after all and he is pretty skilled in chess.
The Black Panther of the Marvel Universe is a rare example of this trope who's a traditional superhero, albeit one that is occasionally under fire from his more-idealistic peers, for obvious reasons.
Calvin and Hobbes parodies this trope, with checkers. Hobbes obliterates Calvin's pieces in one series of jumps, and Calvin spends a few panels staring blankly at the board.
Calvin: "Ah, you've fallen right into my trap! Perhaps you'd like to take that move over?" Hobbes: "Your remaining piece must have one heck of a plan..."
General Wade Eiling definitely fulfills this trope, given the way he manipulates Captain Atom.
In Civil War (2006), Hammerhead organizes a meeting of all supervillains, to be their new leader, replacing the Kingpin. The Kingpin manages to have his plans thwarted... despite the minor inconvenience of being in prison at the time.
In Convergence: Titans #1, Dreamslayer of the Extremists sees himself as one. He recognizes that this whole situation is making pawns out of the heroes and villains, and he'd prefer to be the one manipulating said pawns. True to his word, he pits pre-Flashpoint Arsenal against Troia and Starfire by resurrecting Lian Harper and using her as leverage.
Daredevil: Just about every villain the titular hero faces. The most prominent is The Kingpin, with him and Matthew trying to destroy each other's lives' for years. But beyond him, there's the Owl, the local Mafia gangs, whatever Elektra is scheming whenever she shows up... Even Mysterio resorted in such tactics when facing Daredevil, and he's just a two-bit villain in all other appearances.
DC Comics' Darkseid is also fond of moving figures of his minions and enemies around on a chessboard when hatching his latest evil scheme.
The goddess Athena in DC is a usually heroic and incredibly effective version:
Wonder Woman (1987): Athena's scheme to bring down Zeus required the resurrection of Medousa; the death, by Medousa's stone gaze, of a child of one of Wonder Woman's embassy workers to incense Diana into agreeing to a duel to the death, and then that duel culminating in Wonder Woman's blindness and the decapitation of Medousa. This entire chain of events was simply her way of obtaining a fresh gorgon's head (Medousa's previous head having rotted away to uselessness) to use on Zeus's champion, the hecatoncheires Briareos. And that doesn't even count the plot that she undergoes to consolidate her power once Zeus, Poseidon, and Hades try to rebel... Ares has a conversation with her over a chessboard with pieces reflecting all the players in her plan, and grins when she moves a model of himself before he'd agreed to play along.
The very different version of Athena in the New 52 is manipulating things without any of the other members of the Dodekatheon noticing, in order to put the newly reincarnated version of Zeus back on the throne.
Deadpool has shown many times that, were it not for his insanity, he would be one of the Marvel Universe's greatest Chessmasters. And even with it, he's shown himself several times to be a cunning and dangerous opponent. In his tie-in to the Secret Invasion arc, he joins up with the Skrulls and gets them to add his regenerative abilities to their Super Skrulls, resulting in them regenerating so much that they explode due to not having Deadpool's cancer to keep the regeneration in check. He knew would happen. And this is all a cover so he can hack into the Skrulls' information and find out a way to defeat them for Nick Fury. And the plan was all his.
In Death of the Family, The Joker has spent his year-long absence becoming this. The Catwoman story even shows the chess motif!
The Phantom Blot is (often) at least as close to a Chessmaster as the writers of Disney Mouse and Duck Comics can manage. If there's an unseen mastermind affecting the events and leaving Mickey Mouse baffled for most of the story, it's probably the Blot.
The very first time we see Doctor Doom, he's toying with chess-piece replicas of the Fantastic Four, so that tells you all you need to know. He's usually ranked as Reed Richards' evil doppelganger regarding intellect, and his plans range from the complicated to the really complicated to the one that played both Mephisto and Doctor Strange like Stradivarius violins. Simultaneously. With one move.
An issue of Excalibur parodied the characters-as-chess-pieces visual metaphor, with the characters standing on a chessboard, and Captain Britain saying "Call me paranoid, but I think we're being manipulated."
Probably also a reference to a classic earlier Captain Britain storyline, where the same manipulator, Merlin, played a quite literal game of chess with the characters' fates. He continues to do so during a pivotal story arc of Excalibur, including a time in which he fakes his own death and has his daughter Roma (who's not in on the deception) play the game in his place for a while. When he returns (in the very issue with the above-mentioned cover), he's carrying a chess piece representing Roma, and places it on the board.
Two-Edge of ElfQuest is probably one of the most ridiculously skilled chessmasters in fiction. He forges enough armor and weapons to fill an vault, them makes an exceptional weapon with a secret key to the vault in the pommel, gives it to someone who couldn't use it so that they would be quick to wager it in a game of dice, then tells a third, unrelated person about the key in order to lure the sword's owner into looking for it. That's the simplest and shortest chain of events that Two-Edge is explicitly responsible for. If you count the ones where he's only implied to have been involved, the only events in the entire plot that don't have his fingerprints on them are the ones that occurred before he was born.
Marvel's Grandmaster can come up with some really complicated schemes. Luckily for the heroes he really doesn't care about losing, he just does it for fun. And when he really wants something he's nice enough to let them think they won.
Hellblazer — If you're ever associated with John Constantine, chances are you're already dead.
Celebrated more in Justice League Dark, where Constantine's has a full arsenal of pieces, albeit he calls it a "band" rather than chess pieces.
A perfect example was during the Reasons to be Cheerful arc. John's demonic children attempted to kill everyone that John has ever met and knew. That includes his family, close friends, and those he hasn't seen for a long time. They almost succeeded.
The goddess Athena in the Marvel Universe series The Incredible Hercules is another heroic version of this trope; one of the series' major ongoing threads is a (and, as yet, largely unknown) Batman Gambit she is in the process of executing. Her brother Hercules, a frequent key piece on her chessboard, finds her refusal to be upfront with her plans annoying.
The Incredible Hulk: Bruce Banner is this, at least under Greg Pak's pen. As we learn in Fall of the Hulks, Banner's just as dangerous as his savage green alter-ego — if not more so.
In The Invisibles, there is an extremely mysterious and shadowy character known as the Blind Chessman who, well, plays chess, both literally and metaphorically. It also doubles as a Blind Seer.
Iron Man: Obadiah Stane did a masterful job of bringing every part of Tony Stark's life crashing down. Chess was the theme of his campaign against Stark; he went so far as to outfit his henchmen as Knights, Bishops, and Rooks, with appropriate gimmicks. It's revealed in his origin story that he began playing chess at a young age, and at age eight won a school chess tournament by slitting the throat of his opponent's dog and stuffing the body into the kid's locker. The victory only cemented his obsession with the game.
JLA/Avengers has Metron and The Grandmaster as such.
Judge Death is portrayed this way in the Judge Dredd prequel series The Fall of Deadworld. He's mostly an Orcus on His Throne and only makes sporadic appearances, but seems to be anticipating various events somehow. At one point, he's actually shown hunched over a chessboard with ghoulish pieces reflecting different characters, knocking one off the table after someone was just caught as a traitor.
The Mighty Thor: Odin has sometimes been seeing poring over a chessboard with the characters as the pieces (ususally to show he's going through a morally ambiguous phase).
Now Kid!Loki has been doing it too. He's got figurines of several people that he's dealing with, and uses a map as his chessboard. However, it was drawn at too far an angle to see what he was arranging. When he was turned mortal for a while, these turned into RPG miniatures and (door stopper) rulebooks, but when asked he called it a game of his own devising. So apparently Loki plays an elaborate game of "Calvinball" with the universe.
Mother Freya, the goddess of love in Mark Crilley's Miki Falls, is eventually revealed to be one of these.
Moriarty: James Moriarty is a brilliant criminal mind who is able to create complex schemes in order to get ahead
Metron of New Gods, who is an Ensemble Dark Horse thanks to his unemotional, bipartisan manipulation of events.
Alex Wilder of Runaways. It turns out that, not only did he learn the truth about his parents a full year before the other kids, but he set up virtually every single event in the first volume of the series.
Sunspot shows during his stint leading the New Avengers that he has a deviously cunning mind hidden under his devil-may-care attitude. Any time it seems like he's backed into a corner it's revealed that it's all part of his plan, or he has plenty of backup plans to get him out of trouble. SHIELD tries to take over his island base? He has an entire second base just in case. SHIELD puts a double agent on his team? Wrong, they're a triple agent loyal to Sunspot. The Maker bugs his base and strikes him when his defences are low? Nope, he knew about the bugs, fed the Maker incorrect information to lure him into attacking, and also bugged the Maker's base in return so he knew the Maker's backup plans and how to counter them. It's not just his ridiculous wealth that got him into a leadership position.
Superman: Brainiac has often been this, in contrast to Magnificent BastardLex Luthor. Brainiac has frequently set up incredibly complex plans, using every character as a chesspiece in his efforts to steal cities / become a god/absorb the sum total of all knowledge in the universe (his motive keeps on changing), but has trouble changing them once something goes wrong.
Superman: Red Son has Lex Luthor (naturally) and Brainiac. Superman, on the other hand, is more of a chess novice... He's good, but he's not Luthor good. Or so it seems. As it turns out, he might actually be better.
Luthor's introduction as the Chessmaster in Red Son isn't entirely subtle, but effective: he's just won fourteen simultaneous games of chess on his coffee break, while also reading Machiavelli and teaching himself Urdu by tape (in a tape player he designed himself that morning, no less) "to keep my mind occupied". How good is "Luthor good"? The end sees Brainiac destroyed, (and apparently Superman too), the world united and ready to accept "Luthorism" to lead it. He regards the chessboard and remarks "It's like it was planned to the tenth decimal point forty years ago." Even though Superman survived, Luthor still won the ideological battle, as Superman opted to spend the result of his multi million year lifespan Clark Kenting.
And what ticked him off more than anything? His Superman Clone beat him at Chess. This foreshadows Superman's final escape from his last death trap.
The Ten-Seconders: The Scientist has orchestrated almost everything that happened throughout the series so that he could both dispose of his fellow "Gods" and destroy the Sufficiently Advanced Aliens who created them to take their power for himself.
Thanos is a staple Chessmaster in many cosmic crossovers in the Marvel Universe. It's frequently lampshaded how other characters (especially heroes) exist solely to be manipulated by him for whatever agenda he might have at the moment.
The Ultimates: General Nick Fury is a heroic (well, anti-heroic) version of this trope with the full sanction of the United States Government. And also, total badassery.
The regular Marvel Universe's Colonel Nick Fury is no slouch either, even when he loses the support of the US government.
Ultimate X Men: Xavier had planned the events of the first two arcs. This gave him several victories: the Sentinel program was shut down, he got in good relations with the White House, Magneto was removed from the scene, and Weapon-X was closed.
V, Anti-Hero of V for Vendetta. In the film, Finch actually figures out part of the plan, but can't do much to stop it by that point.
In the graphic novel, Finch goes as far as to almost stumble upon V's lair, but decides his ordeal is over when he fatally shoots V. This was all part of V's plan....
V also uses a Domino motif for his plan.
Tao from the Wildstorm comics universe, especially as written by Alan Moore or Ed Brubaker.
Cyclops from X-Men, the "General of the Mutants", is the current main page image. He's also a deconstruction of the trope. While his grand plans allows him to get the job done, it also served as the catalyst for the more recent split of the X-Men, with Wolverine leaving with half of the team out of disgust due to Cyclops using members as pawns. Since this left him with the members who were perfectly willing to go along with his plans, if anything this actually cemented his position.
Y: The Last Man has the Daughters of Amazon led by Victoria, a master of chess; they argue, among other things, that the queen is the most powerful chess piece, like women are the superior sex.
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