A book cipher is a type of cipher that generally uses a book or other large amount of text to encrpyt a message. In order for the encrypted message to be decoded correctly, both the sender and receiver need to use not only the same book, but to make sure to use the same edition of the book.
Traditionally, book ciphers work by giving the locations of each word of the message inside the book used for the key. The method of locating the words used in the cipher can vary greatly between uses. If a novel is used as the key, then the code could be written as "1:23:5" with the first number being which chapter the word is in, the second number listing which paragraph in that chapter, and the third number being the word in that paragraph. The cipher will have one of these sets of numbers for each word in the message, and the sets are not limited to what can be used to point to the word. For example, instead of using chapter:paragraph:word, the cipher could use page number:column on page:number of lines down the column:word on that line.
In 3301's puzzles, instead of using a word the book ciphers give the location of a single letter or character which are then joined together to make a word. This is necessary as one of the book ciphers' solutions is the URL of an Onion hidden service.