The Book Cipher

This is an old and basic cipher.

John Doe has a copy of a book. Richard Roe has a copy of the same book. To send Richard a coded message, John generates a series of number triplets. The first number is a page, the second number is a line on the page, and the third number is the word inside that line. (It can also be just page and word, if you want to make it easier, and less secure.) When he receives the message, Richard takes out his copy of the book and gets to work looking things up.

Big and well-known books make better sources as you have more words to choose from (thus The Bible is often the source), and no one will react if you're walking around with a pocket version of "The Da Vinci Code". (It also makes it easier to have two copies of the same edition -- an absolutely critical requirement as there's no guarantee that everything will line up the same between two different printings, let alone different editions from different publishers.)

If you're walking around with an Older Than Radio edition of a book, however... people will get suspicious (especially the detective who's after you).

The Ottendorf Cipher is a variant coding page, word and letter within the word. Another variant is to use The Bible and code for book, chapter, verse and either the word or the letter.

Examples of The Book Cipher include:

Alternate Reality Game

In Lost: Mystery of the Island, a series of four jigsaw puzzles released in 2007, Ottendorf cipher was used on each puzzle's box to hide spoilers and reveal information about the show to the fans.

Anime and Manga

In Naruto, Jiraiya uses a book cipher referring to his own novels to convey information about Pain.

Comic Books

A Detective Comics story "And the Executioner Wore Stiletto Heels" involved the villain, Stiletto, using an obscure book about shoes for a cipher (the villain chose this book as a pun on his name—think "stiletto heels"). When Batman goes to the bookstore, the owner mentions how strange it is that he just sold several copies of a book nobody would buy normally. Batman asks him who bought the book in order to learn who's in on the plot.

Film

In National Treasure, the hero discovers various numbers hidden on the back of the Declaration of Independence; these correspond not to a book per se, but to the 'Silence Dogood' letters his father donated to a museum.
In the film Unknown, Prof. Bressler's passwords are obscured by an Ottendorf cipher.

Literature

This is described and used in The Curse of Chalion by Lois McMaster Bujold.
In The Valley of Fear, Sherlock Holmes decrypts a message enciphered with a book cipher by deducing which book had been used as a key text.
The name of Ken Follet's World War II thriller The Key to Rebecca refers to a German spy in Cairo using Daphne du Maurier's novel Rebecca as the basis of a code.
In A Presumption of Death, Lord Peter Wimsey, on assignment for British Intelligence in WWII Nazi-occupied Europe, uses a code based on the works of John Donne. The Germans, suspecting that an intelligence service in which Oxonians have a major role would choose a classical work of English literature, systematically try such works until hitting the right one and breaking the code, coming near to catching the spy. Wimsey then improvises a new code, based on an unpublished text known only to himself and his wife.
Another Wimsey example at one remove is in Have His Carcase, using a Playfair Cipher with the keyword (the tenth word on page 583 of the latest edition of a Chambers' Dictionary) disclosed this way.
Graham Greene's heroes often use book codes. In The Human Factor, several books are used, and an edition of Charles Lamb's Tales from Shakespeare is used in Our Man in Havana.
The heroes of the Matthew Reilly novel Six Sacred Stones used a book cipher to send confidential messages to each other. The key text was the Harry Potter books, but the messages were sent via a Lord of the Rings forum to make the key text harder to identify.
The German spy uses this kind of encryption in The Death of Achilles.

Live Action TV

In the second episode of The BBC's Sherlock, they encounter a number of symbols. This turns out to be numbers written in an ancient Chinese script, with the book being a Tour Guide of London (which ends up as part of Fridge Brilliance, as the Chinese Gang use these symbols to arrange meeting points.
In the Season 2 finale of BBC's Luther, the numbers in a notebook is revealed to be this. The book they use to decipher is the Bible that Luther finds at the hotel room of the culprit.
A book cipher plays an important role in the TV version of Sharpe's Sword. The key text is Voltaire's Candide.
"The Fisher King", a two-part episode of Criminal Minds, features an Ottendorf cipher part of a larger puzzle to find a girl who had been missing for two years. The key text was The Collector by John Fowles.
Burn Notice uses this, especially in the fourth season, where it becomes part of the season-long plot when Michael Westen steals a Bible from a safe deposit box that is the code book of Simon.
In The Unit episode "Paradise Lost", Jonas Blane uses a book code from the poem Paradise Lost to communicate to his wife, Molly, that he has arrived safely in Panam.

Real Life

The infamously unsolved Taman Shud case seems to involve a "one-time pad" cipher using the edition-and-page method with a specific edition of the Rubaiyat of Omar Khayyam. Unfortunately, there's some other element of the key that has never been determined, so the cipher remains unsolved.
The Beale Ciphers are possibly a case of this. At the least, the second of the three documents, the one indicating the contents of the treasure, maps to the letters in the Declaration of Independence. Of course, there's also some evidence that it was a hoax from the start.