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."

Matrix, Trinity, and Morpheus are all makes and/or models of music synthesizer.

Almost every line spoken by Neo's "customer", Choi, in the beginning of the film is foreshadowing: "Hallelujah. You're my savior, man. My own personal Jesus Christ." "Yeah, I know, this never happened. You don't exist." "Hey, it just sounds to me like you might need to unplug, man."

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"! Sound familiar?

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 king who was visited by troubling dreams.

Neo is an anagram for One.

In the scene where Neo is asleep at his computer, which scrolls various news articles about Morpheus, one of the 'newspapers' is the "Courier New Press." Courier New is the name of a common computer font.

References to Alice in Wonderland are abundant throughout the movie. "Follow the white rabbit." "I imagine that right now you're feeling a bit like Alice, tumbling down the rabbit hole?" "You take the red pill and you stay in Wonderland and I show you how deep the rabbit-hole goes." Neo also goes 'Through the looking glass' when he dips his hand into the mirror that grows on him. The Red pill and the blue pill are very reminiscent of the 'drink me' potion and 'eat me' cake from the book. Coincidentally, 1999 is the Chinese Year of the Rabbit. "A generally pleasant year which will bring new hope to the lives of many"(!)