Watson is called "John H. Watson" in the Sir Arthur Conan Doyle stories, except for one brief scene in "The Man with the Twisted Lip", when his wife calls him "James". This puzzled scholars for years until Dorothy L. Sayers suggested that the "H" stood for "Hamish", the Scottish equivalent of "James". In the film, Watson's middle name is "Hamish".
The text of the note that Holmes leaves Watson on the packing crate reads: "Come at once if convenient. If inconvenient, come all the same." This quote is taken directly from Holmes creator Sir Arthur Conan Doyle's short story "The Adventure of the Creeping Man".
In 2003, Stephen Fry appeared on the UK quiz show Celebrity Mastermind. His special subject was Sir Arthur Conan Doyle's Sherlock Holmes, including a question on Mycroft Holmes. He chose this topic, because he loved Sherlock Holmes stories as a child, and at the age of ten, was the youngest member of London's Sherlock Holmes Appreciation Society.
At the end of the train sequence, Watson says to Holmes, "Once more unto the breach". This is a line from a speech in Henry V by William Shakespeare. Much later in the play's speech, Henry V also exclaims, "The game is afoot", which Holmes used as a catchphrase in Sir Arthur Conan Doyle's stories.
The series of numbers on Moriarty's blackboard (and seen again briefly during the notebook decoding sequence towards the end), is Pascal's triangle with the shallow diagonals marked, the sums of which form the Fibonacci sequence.
In Paris, Professor Moriarty picks up a newspaper (the Daily Graphic). On the back of the paper is an ad for "Lazenby's Soup Squares". At the end of the movie, Holmes, while speaking to Moriarty, says "On Her Majesty 's Secret Service", the title of the Ian Fleming James Bond novel, and the only Bond film starring George Lazenby.
After the attack in the train, Holmes' lipstick is smeared across his mouth. This makes him look somewhat like the Joker from The Dark Knight (2008), the role for which Heath Ledger was awarded a posthumous Academy Award. One of the actors he beat out for the award was Robert Downey, Jr. from Tropic Thunder (2008).
The trivia items below may give away important plot points.
Robert Downey, Jr. came up with the idea for the disguise as a cross-dresser, which was originally a priest. Whether Downey knew it or not, in "The Adventure of the Mazarin Stone" Holmes is said to have disguised himself as an old woman.
Sherlock defeats Moriarty by pulling him over Reichenbach Falls, with both of them falling to their apparent deaths. Holmes is later shown to have survived. In Sir Arthur Conan Doyle's story "The Final Problem" (intended to be the final Sherlock Holmes story), Holmes defeated Moriarty in the same way, by falling over a waterfall to the apparent death of both. However, in response to overwhelming public demand, Doyle wrote another story and resurrected Holmes.
The medals Watson wears during his stag party are the Afghan War Medal (red and green ribbon) and the Kandahar Bronze Star (multi-colored striped ribbon), which would make Watson a veteran of the Second Afghan War (1878-1880).
In Holmes' final struggle with Moriarty, he uses a two-handed clasp to immobilize Moriarty before going over the falls. In the 1903 short story "The Adventure of the Empty House", Holmes does not specify the specifics of the fight, but the illustrator of the story, Sidney Paget, drew Holmes in the same unique grasp that Robert Downey, Jr. used in the film.
During the scene in which Holmes, Watson, and Sim (Noomi Rapace) are to travel across the border on horseback, but Holmes opts to ride a pony, the soundtrack becomes an homage to that from Two Mules for Sister Sara (1970), in which Shirley MacLaine's character chooses to ride a burro, while Clint Eastwood rides a horse.
The chess game between Holmes and Moriarty was based on a real match between Bent Larsen and Tigran Petrosian in 1966 in Santa Monica. The game had a Queen sacrifice, and discovered checkmate to win the game. The opening moves are slightly different, and the colors have been reversed though.
The movie is primarily based on the short story "The Final Problem" by Sir Arthur Conan Doyle (and to a lesser extent on "The Empty House"), but also shows aspects from other Sherlock Holmes stories: "The Sign of Four" (introduction of Watson's fiancée); "The Greek Interpreter" (introduction of Mycroft Holmes); "Valley of Fear" (explanation of Moriarty's underworld empire); "The Speckled Band"; "The Dying Detective"; "Bruce Partington Plans"; and "The Second Stain".
The opera that the characters visit in Paris is "Don Giovanni", by Wolfgang Amadeus Mozart. The scene being played, is the finale of Act II. In it, the villain and seducer Don Giovanni is visited by the animated statue of one of his victims, who drags him to Hell when he refuses to repent.
The world's last sea-going paddle steamer, the P.S. Waverly, is seen when Holmes and Watson cross the English Channel. The P.S. Waverly is docked, and in regular use on the River Clyde, Glasgow, Scotland.
The chariot that delivers Holmes, Watson, and Simza to the anarchists' headquarters, is named "Les Sept Grenouilles" (The Seven Frogs). This is a good disguise for gypsies, since they don't like frogs.