When banks totter and stock markets do kamikaze impersonations, some SF fans remember the 1970 R.A. Lafferty story that begins: "There is a secret society of seven men that controls the finances of the world. [...] There are some who believe that it would be better if one of those seven were a financier." ("About a Secret Crocodile", August 1970 Galaxy)
All the best conspiracy theories agree that Secret Masters run the world. According to David Icke they're giant space lizards posing as the Royal Family, though there's the worrying possibility that Icke doesn't think he's writing science fiction. More traditionally it's the Bavarian Illuminati, as deliriously revealed, complicated, refuted and disinformationed in Robert Shea's and Robert Anton Wilson's Illuminatus! trilogy. (They even managed to sneak one of their eldritch Masonic symbols onto the dollar bill!) In Little, Big by John Crowley, US politics is controlled by a cabal of men in suits called the Noisy Bridge Rod and Gun Club, which is maybe too plausible to be funny. Even more convincing, until the sinister organization was abolished in 2002, was Tom Holt's dark suggestion that we're all puppets of the Milk Marketing Board.
I have a weakness for ultra-dotty conspiracies that turn out to be shaggy dog stories, like GK Chesterton's The Man Who Was Thursday and A.E. van Vogt's Weapon Shops of Isher books. What these have in common is that the two opposed sides (anarchist bombers versus police, libertarian gun merchants versus oppressive Empire) are secretly run by the same godlike puppet-master. Oops, forgot to say "spoiler warning" there.
Speaking of dottiness, there's an Illuminati card game where everyone gets to play a conspiratorial power-group: the Servants of Cthulhu, the Bermuda Triangle, the Gnomes of Zurich.... Thus, after complex alliances and double-crosses, the International Communist Conspiracy – aided by the Orbital Mind Control Lasers – may well end up as the power behind the CIA. Or, conversely, behind Star Trek fandom.
Sometimes secret masters are literal chess-players, moving us like pawns on the board and giggling at our silly delusions of free will. When this is revealed to the manipulated hero of John Brunner's The Squares of the City, he's only slightly cheered to be told he's not a pawn but a knight.
Still more ego-deflating is the idea that mere animals are in charge. Eric Frank Russell wrote this story twice, with dogs running the show in "Into Your Tent I'll Creep" and camels in "Homo Saps". Camels are also famously hyperintelligent in Terry Pratchett's Pyramids, and so of course are mice in The Hitchhiker's Guide to the Galaxy. When the protagonist of Fredric Brown's "Come and Go Mad" learns that the black, red and white factions that secretly control Earth are the ants, he goes ... oh, you guessed.
Not all authors take Secret Masters seriously. William Tenn mocked the idea of a hidden power behind the throne in "The Servant Problem", where supreme ruler A is secretly controlled by B, a puppet of C, who's unknowingly in the power of D – and D is helplessly loyal to A. In John Sladek's The Muller-Fokker Effect, dedicated conspiracy theorists struggle to decipher messages they're sure were embedded by devious Commies in the endless decimal places of pi. Jorge Luis Borges's very short "The Sect of the Phoenix" describes a furtive and slightly disgusting cult which (readers gradually come to realize) includes the entire human race. With the possible exception of the Milk Marketing Board.
David Langford denies being a Secret Master of Fandom. Well, he would, wouldn't he?