Carrie-anne Moss (Trinity) played Liz Teel in the TV series "Matrix" (1993).
In the first minutes of the film during the scene in which Trinity is chased by one of the agents and she leaps from one house to the next, an advertisement saying "GUNS" can be seen on the second building. The gun pictured in the ad is exactly of the same make and model (Israeli Military Industries' Desert Eagle) as the guns used by all agents during the film.
In the movie Higher Learning (1995), Laurence Fishburne's first sentence was: "Welcome to the real world."
Cypher is a play on the name Lucifer - the devil.
As Neo runs through the old lady's apartment near the end of the film, we see an image on the TV of a menacing man in a black suit coat. The image is that of one of the Number 2's from the TV show "The Prisoner" (1967).
When Neo is calling to get extracted from the Matrix, he says, "Mr. Wizard get me out of here," a reference to the 1960's cartoon Tooter Turtle. Each episode, Tooter would yearn to be something he wasn't and have his friend Mr. Wizard (a lizard) wave his magic wand and make him an astronaut or a scientist or whatever. Inevitably, Tooter would quickly get himself into trouble and call out "Help Mr. Wizard," and the lizard would intone "Drizzle, drazzle, druzzle, drome, time for this one to come home." Tooter would be transported back to his old self and be chided by Mr. Wizard to "be happy with what you are."
The glyphs on the computer screens, with the exception of the call traces, consists of reversed letters, numbers, and Japanese katakana characters.
All of the references to street corners (e.g. Wells and Lake) are real intersections in Chicago, USA, the Wachowski brothers' hometown. The subway train has signs for "Loop," another Chicago reference. The film however is quite obviously not set in Chicago or any other real city (though it was filmed in Sydney).
Neo produces a computer disk from a book titled "Simulacra and Simulation," an actual work of critical theory that deals with issues of what is "real" and what is "simulation or simulacra." When Neo opens the book, he opens to the chapter, "On Nihilism."
Inside the Nebuchadnezzar there is a brief shot of a plaque with the ship's name, above which it says "Mark 3 no. 11." The Biblical verse Mark 3:11 is, "And whenever the unclean spirits saw him, they fell down before him and cried out saying, 'You are the Son of God.'"
Neo is an anagram for One.
Check out the room numbers for Trinity and Neo. When the cops bust in on Trinity in the opening scene the number is 303 ("trinity" 3) and since Neo is The One the number of his apartment is 101.
Coincidentally (or not), Matrix, Trinity, Morpheus, 303 and 101 are all models of music synthesizer (from various manufacturers).
Almost every line spoken by Neo's "customer" in the beginning of the film ("You're my savior," "You don't exist," etc.) is foreshadowing.
When Neo is meeting with the Oracle, the music playing in the background in her apartment is Duke Ellington's "I'm Beginning to See the Light," a reference to Neo's continued awakening.
When the traitor meets with agent "Smith," we learn that his name is Reagan. He says he wants to be someone important, maybe an actor, and that he wants to "remember nothing"! Sounds familiar? Former U.S. President Ronald Reagan was once an actor and now suffers from Alzheimer's disease.
In the Oracle's waiting room, the television is showing white rabbits (which, at the beginning of the film, Neo was instructed to follow) from Night Of The Lepus.
Names of people and objects have historical significance, all related to dreams and illusions. For example, "Morpheus" (film character) was named for the Greek god of sleep and dreams; and "Nebuchadnezzar" (hovercraft in film) was a biblical Babylonian king who was instructed by God in dreams to destroy the inhabitants of Jerusalem because they worshipped false prophets.
Biblical interpretations continue: The name Thomas means "twin", but the apostle Thomas also had the epithet "the Doubter." Thus "Thomas Anderson" could be interpreted as "the doubting Son of Man." Or possibly "twin of the Son of Man," whichever seems more interesting. What earned the apostle this particular epithet was that he allegedly wouldn't believe the resurrection of Christ until he had put his hand into the wound in Christ's side. In the end of the movie, Neo dives hands-first into the side of Smith, who then (violently) sort of turns into Neo. So he put his hand into the side of himself, the Son of Man.
Other parallels with the life of Christ: Neo taken to a large building and tempted to jump off it; Neo ascending above the street (c.f. Christ's last appearance in the Acts of the Apostles).
The license plate number of the Agents' car is 70858. Coincidentally (or not?), Kevin Bacon's birthday is 7/08/58.
When Neo is fleeing from the agents through a marketplace, one of the agents fires at him and misses, exploding a pile of watermelons nearby. This may be an homage to an identical scene in Ghost In The Shell.
Before filming, the principal actors spent four months with martial arts experts, learning very complicated fight moves.
The song that Neo wakes up to at the start of the film is "Dissolving Child" by Massive Attack.
The brothers who helped the crew while they were in the Matrix, were named Dozer and Tank. Could this be a reference to "Fraggle Rock" (1983), in which characters called Dozers (who built things for the Fraggles) drove small tanks?
The mobile phone used most of the time during the movie is the Nokia 8110i.
The number of the phone Trinity was using at the beginning of the movie is 555-0690.