The Book: 11/22/63, by Stephen King
The Gist: A schoolteacher travels to 1958 through a portal hidden in the pantry of a diner to prevent the president's killing.
The Theory: The Warren Commission was right. Lee Harvey Oswald was a lone, Cuba-loving nutjob.

The Book: American Tabloid, by James Ellroy (1995)
The Gist: Real figures like J. Edgar Hoover, Howard Hughes, and Marilyn Monroe mingle with fictional characters in a speculative take on events leading to Kennedy's death.
The Theory: A consortium of mafiosi, anti-Communists, and rogue CIA agents all sought to get rid of JFK, with motives ranging from revenge for the Bay of Pigs to ending RFK's mob investigations.

The Book: Libra, by Don DeLillo (1988)
The Gist: A CIA researcher pieces together details about Oswald's life and the events of that fateful day.
The Theory: Rogue agency elements and Cuban exiles, seeking to permanently poison relations between the U.S. and Fidel Castro, recruited Oswald for an assassination attempt designed to fail—then changed course and decided to go through with the plot.

The Book: The Tears of Autumn, by Charles McCarry (1974)
The Gist: Convinced that international forces were behind the shooting, an ex-CIA operative (like the author himself) circles the globe trying to figure out who did it.
The Theory: The South Vietnamese carried out the assassination to avenge the U.S.-backed murder of their own president, Ngo Dinh Diem, just three weeks earlier.

Also on
Three Novels to Read Now
Arthur Goldwag, Cults, Conspiracies, and Secret Societies
Q&A: Don DeLillo