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• Actor Allusion:
  • Keanu Reeves starred in Johnny Mnemonic, as a character who could have a jack placed straight into the back of his head. It is also a film about telepresence.
  • Joe Pantoliano lying about a car accident in a movie directed by the Wachowskis... why is that so familiar?
  • Monica Bellucci stands in front of a TV playing The Brides of Dracula when she pulls a gun on her henchmen in Reloaded. Monica was one of the vampire brides in Bram Stoker's Dracula.
• Development Gag: A deleted subplot from The Matrix reveals that Morpheus has previously believed five other people to be The One, all who died after attempting to fight the Agents. In The Matrix Reloaded, the Architect explains that there have been five previous versions of the Matrix before the current one, each with its own version of the One, meaning that Neo again has five predecessors.
• Doing It for the Art: While watching the "Lady in the Red Dress" scene, some may notice the same people passing Neo and Morpheus more than once. Production goof? Nope, all extras in the scene are actual twins. They searched all over Sydney for twins and brought them in to demonstrate how Mouse, writing the Agent training program, got lazy and just copy-pasted the same models over again instead of making unique ones. Did you notice that... or were you staring at the lady in red?
• Dyeing for Your Art / Important Haircut: "Spoonboy"'s mum was very reluctant to have his beautiful locks shaved off.
• Executive Meddling: Dropping the original idea of Human Resources being a vast neural net for the more literal concept of human batteries because Viewers are Morons. Giving all the other stuff that has to be explained (or not) in this trilogy, one wonders why this idea was so difficult to put across.
• Hire the Critic: For The Ultimate Matrix Collection, the filmmakers included two Alternate DVD Commentaries, one by philosophers who loved the movies, and one by critics who hated them.
• Killer App: The Matrix was this for the DVD format.
• The Other Darrin: Mary Alice replaces Gloria Foster as the Oracle in Revolutions, as Foster died shortly before filming began. It's justified in-universe with a story about Ramachandra selling her original shell's termination code to the Merovingian in exchange for his daughter's safety.
• The Other Marty: Aaliyah was originally cast as Zee, but she died in a plane crash in the midst of filming her role; her completed scenes were reshot by Nona Gaye.
• Recycled Set: Sets from Dark City (1998), including rooftops, buildings and others exteriors sets, were used in this film. The rooftops that Trinity runs across at the beginning of the film are the same ones that John Murdoch runs across in Dark City.
• Shout-Out:
  • The "bring it" gesture both Trinity and Neo make is from Bruce Lee.
  • The Oracle's focus on and use of cookies is almost certainly a shout-out to one of the very first computer viruses, The Cookie Monster, which would simply take over a computer or terminal asking for a cookie, and would not relinquish it until "cookie" was typed into its prompt. (It's in part because of The Cookie Monster that the session-information files saved by websites are known as "cookies".)
• Star-Making Role: For Carrie-Anne Moss, who was almost completely unknown before she became Trinity. Laurence Fishburne, Hugo Weaving and Monica Bellucci in particular, going from semi-obscure straight into the mainstream after this movie. For Keanu Reeves, however, this was more of a Type-Cementing Role.
• Trope Namer: This series named the following tropes:
  • A Glitch in the Matrix
  • Matrix Raining Code
  • Matrix Hypothesis, a subset of Recursive Reality
  • Red Pill, Blue Pill
  • Answers to The Name of God, formerly named "Smith will suffice"
  • Your Mind Makes It Real
• Throw It In: After the lobby shootout, the camera pans back showing the aftermath of the gunfight in the lobby. During this, a piece of one of the pillars falls off. This happened by coincidence during the filming and was not planned, but was left since it seemed appropriate.
• What Could Have Been:
  • Originally, Will Smith was offered the role of Neo, but turned it down for his part in Wild Wild West. Smith explained his decision in 2004, in an interview in Wired: "You know, The Matrix is a difficult concept to pitch. In the pitch, I just didn't see it. I watched Keanu's performance –- and very rarely do I say this –- but I would have messed it up. I would have absolutely messed up The Matrix."

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