Alice and Bob note cartoon by John Richardson in Physics World, March 1998
When the interaction between two hypothetical characters is needed to explain or describe some system, they are nearly always called Alice and Bob. Alice and Bob — A and B. This duo originally started out as a standardized way to explain cryptography. Over time, the duo has been adopted in explanations of mathematics, physics, quantum effects, and other arcane places, but have also been seen in fiction.note They are also found in a surprising number of trope definitions. We're trying to get them cleaned out. Feel free to pitch in.
Where more than two characters are needed, other names are used, such as Carol and Charlie. Some names have acquired standard meanings, such as Eve the Eavesdropper. Lists of these can be found in Bruce Schneier's book Applied Cryptography, and at that other wiki.
See also Those Two Guys, Greek Chorus.
In most cryptography textbooks, communications are presented as being between Alice and Bob, and must be secured from a third-party interloper named Eve (for Eavesdropper, of course!). If the problem requires the involvement of more than two parties, then Charlie and Donna may be introduced. This is the basis for the XKCD reference. Other character names sometimes used for special purposes include Mallory (a malicious active adversary, capable of changing the messages sent between Alice and Bob, whereas Eve merely listens), Trent (a mutually trusted third party, whom Alice and Bob might prevail upon to execute protocols in which they don't trust each other), and Peggy and Victor (the prover and verifier, respectively, in zero-knowledge proofs).
Game Theory books often use an adaptation of Alice and Bob in "Rose and Colin" (rows and columns on game theory charts), with "Larry", or "layer" thrown in for three person games.
Game Semantics books tend to use Abelard and Eloise (for resemblance to the universal and existental quantifier symbols, which are an inverted A and a backwards E). They are also the names of a medieval logician and his lover.
Alice and Bob are the names of the parents in Vernor Vinge's Rainbows End, and a government official is named Eve Mallory.
E. R. Emmet's "Our Factory" puzzles feature "Alf", "Bert", "Charlie", and so on.
In Tae Kim's Guide to Learning Japanese, a free, online textbook, Alice and Bob are the main characters used in example dialogues and mock conversations, posing as foreign exchange students in Japan.
One of the logos at the end of The Bonnie Hunt Show (2008-2010) is for "Bob & Alice Productions". Bonnie's Hunt's parents are named Bob and Alice so it is either just a reference to her parents or both.
Alice and Bob really are quantum- a professor at the University of Washington has used two separate remote cameras, named Alice and Bob, to test the theory of non-locality and its potential for time travel, by attempting to receive a message before it's sent. The experiment hasn't yielded results so far, but it's telling.