Smith - In an early scene in The Matrix Reloaded, Smith drives an AudiA8 with the license plate number "IS 5416"; in the King James BibleIsaiah 54:16 reads "Behold, I have created the smith that bloweth the coals in the fire, and that bringeth forth an instrument for his work; and I have created the waster to destroy". It should be noted that the three Agents' names in The Matrix (Smith, Jones, and Brown) are all very common English surnames.
Neo / Thomas A. Anderson - The word 'Neo' is an anagram of the word 'eon' and the word 'One'. neal ( Νέο ) is also Greek for 'new,' suggesting messianic overtones for his mission in the Matrix. The name "Thomas Anderson" is likely a reference to the gnosticGospel of Thomas and the Greek word for "man", andras (Άνδρας), which, in ancient Greek, is andros in the genitive case. "Thomas" also means "twin," referring to the dual identity of Neo/Thomas Anderson. From "andros-son" we are given the term Son of Man, a direct reference to Jesus Christ. Thomas may also be a reference to Doubting Thomas, the name of an apostle who doubted the resurrection of Jesus Christ at first.
Switch - Switch's name may be a reference to a network switch, or any number of "switches" used in computer technology. Many other Matrix characters' names reference computer technology, such as "Mouse" and "Link". The name Switch could also be a reference to her white clothing ('switched' from the usual black attire worn by the others).
Cypher - Cypher's name may be a reference to ciphering, or encryption, which is commonly done to prevent computer documents and programs from being hacked. Cypher himself is very difficult to understand and his selfishness and treachery is hidden under a facade. The name is also a nod to the hacker subculture, which greatly influenced the first film. Cypher may also be related to Lucifer (Lu-Cypher), the Angelic name of Satan, referring to his actions in rebelling against Morpheus.
Apoc - Short for "Apocalypse", translating to "The Revelation", or "revealing of the truth".
Mouse - A reference to a computer mouse. Also the name of a character in the Hugo Award nominated Science Fiction novel Nova (1969) by Samuel R. Delany. The character Mouse is once called "the little one", implying a play on his name.
Tank and Dozer - References a military tank and a bulldozer. Both are heavy machinery, usually imagined to be unstoppable.
Councillor Hamann - A reference to J. G. Hamann (Johann Georg Hamann), the philosopher.
Councillor West - A reference to, and played by, Dr. Cornel West, the philosopher.
Captain Soren - A reference to Søren Kierkegaard, the originator of the concept and terminology of the "leap of faith" and often regarded as one of the fathers of existentialism. He used the pseudonym Vigilius Haufniensis ("watchman of the harbour), which also links to the ship's name.
Link - In general, a link is something that holds or binds things together. Most likely another reference to computer technology. In computer terminology, a "link" may be a reciprocal link, a hyperlink, a data link, or a hard link, among others.
The Merovingian - The Merovingians were a dynasty of Frankish kings who ruled parts of France and Germany from the 5th to the 8th century AD. According to some fictional accounts, for example the novel The Da Vinci Code, the Merovingians claimed descent from Jesus Christ. The Merovingian is also characterized fairly heavily as Hades. In Greek mythology, Hades is married to Persephone.
Persephone - Greek mythology states that the goddess Persephone (Περσεφόνη) was taken to the underworld by Hades, whose bride she became. Her mother, Demeter (Δήμητρα) , goddess of the harvest, pled for her daughter's company; Hades, moved, allowed his wife to return from the underworld for six months a year. During the other half, Demeter mourns and winter reigns.
The Oracle - The "mother" of the Matrix, as described by the Architect, its primary creator. She is an analogue of the Delphic Oracle. The film appears to make close references to the Delphic Oracle (Μαντείο Δελφών) , including the Latin sign that reads "Know Thyself" over her kitchen door, the three legged stool she sits in (the Pythia sat in a tripod), and even the smell of baked cookies, in that the Pythia breathed in the fumes of the earth which contributed to her prophetic trance. The term is also used in complexity and computability theory: an oracle machine is an abstract machine used to study decision problems; a very apt description of the Oracle's role in the Matrix.
The Keymaker - A program designed to create access points through practically any location in the Matrix.
The Architect - A software architect is someone who designs computer systems at a high level, and the Architect is assumed to have designed the Matrix itself, but was unable to do so alone; hence the Oracle. "The Architect" is also a name for God commonly used by the Freemasons.
Mifune - In honor of Toshiro Mifune, an actor that played many Samurai in Japanese films.
Charra - (defender of Zion, woman with bazooka) Spanish for "cowgirl".
Choi - French for choice (Slightly altered—this is choix). His girlfriend is 'Dujour', French for of the day (Slightly altered—this is du jour). Choix du jour means plate of the day. Alternatively, the name could pertain to Croix de Guerre which means Cross of War.
Zee - Is not a reference to actress Nona Gaye's aunt Zee (short for Zeola), as the character was named before Gaye was cast. Zee is actually a reference to the popular video game series The Legend of Zelda. This game's central character is called Link, and his purpose is to rescue the princess named Zelda.
Sati - A reference to the Hindu figure Sati. Sati often means "Self immolation" or self sacrifice. In the language "pali", 'sati' the state of being mindful, indicating a special kind of consciousness or self-consciousness.