What is the difference between an homage and plagiarism? Well, its a fine line, but take this analogy: when you write a paper and want to reference something someone else wrote, you place a footnote. Most readers gloss over the footnotes without ever looking at them. But they are still necessary to the integrity of the paper.  Similarly, the Wachowski brothers knew they would be derided as having copied aspects of other films. To counter this, they actually put in obscure allusions to those films as their offering of an homage, a sort of 'footnote'.

            First, to poke fun at the contrivances of all formulaic movies, the Source in Revolutions is named 'Deus Ex Machina' in the credits. This is the term used to refer to any resolution to a story which does not pay due regard to the story's internal logic and is so unlikely it challenges suspension of disbelief, and presumably allows the author to end it in the way he or she wanted. The term also is Latin for "god from the machine."

Superman - Neo's last scene is in a phonebooth at end of The Matrix, after which he emerges to fly away, just as Clark Kent goes in a phone booth to fly away as Superman. More explicit is Link's line in Reloaded: "He's doing his Superman thing".

Alfred Hitchcock: Vertigo and Psycho - The Matrix references Vertigo, while Reloaded references Psycho. Both the opening shot of the Alfred Hitchcock classic Vertigo and The Matrix open with a chase across rooftops by cops after a suspect, and some of the same camera angles are used in both. A shot of Neo's own case of vertigo is seen when he steps out on the ledge of his office but then backs away, and then when he must complete the "Jump" program. Also, when the Architect is talking about all the people that will die in Zion, there are clips from TV commercials and other movies on the screens behind him. Among them is a famous black and white clip from Alfred Hitchcock's 1960 film Psycho. 

While Hitchcock's movies are obviously completely different in terms of plot and genre, they are referenced by the Wachowskis because they often share similar themes:

- Paranoia about the police. Throughout the movies, there is a pervasive fear of the Agents as the antagonists. Watch Psycho and compare the cop that follows Marion around to the Agents in The Matrix.
- The guilt of the ordinary person trapped in a criminal situation. Hitchcock employed this theme throughout most of his movies. It is also seen in the Matrix trilogy, but mainly in the first film (i.e. when Neo is confronted by the Agents in the beginning).
- The integration of the audience into the movie. When Psycho was released, for example, the ads said "Do not reveal the surprises!" "I was directing the viewers," Hitchcock said. "You might say I was playing them, like an organ." Hitchcock loved to make the audience an active participant in his movies. Similarly, the matrix movies attempt that same effect, even filming things like Neo flying into the audience at the end of The Matrix.
- Substituting protagonists. Starting a character as the hero, and then removing them from the picture. Like Morpheus, Hitchcock did this (more adeptly) in Psycho. Marion Crane, the apparent protagonist of the movie, is killed only a third of the way in. Similarly, Morpheus is relegated to sidekick after The Matrix, the first third of the trilogy.
- And of course, the fear of disappointing one's mother. This fear drives and paralyzes Norman Bates, causing his insanity. It is also found somewhat in the relationships of Neo and Smith to the Oracle.

Terminator - the red eye of the spider pulled out of Neo's stomach in The Matrix fades as it is turns off, just like the eyes of cyborgs in the Terminator series.

Star Wars - The scene where the sentinels come for the first time in The Matrix is a reference to The Empire Strikes Back. It's a combination of the scenes where Lando and Chewie fly the Falcon after getting Luke's hand fixed, and the asteroid field scene. Luke, having just gotten a new hand, limps in the cockpit with Leia; in The Matrix, Neo just woke up and hobbles in with Trinity. The cockpit is almost identical, and Morpheus says Star Wars lines from the asteroid field scene, "Set her down there" and "Here they come." Also, in Revolutions, Niobe flies through the tunnel like Han Solo with the Millennium Falcon.

The Prisoner - As Neo runs through the old lady's apartment (near the end of The Matrix) we see an image on the TV of a menacing man in a black suit coat. The image is that of "#2", a character from this TV series. Also, like the main character "#6" of the series, Neo is the 6th version of the One.

The Avenging Fist - this is a Hong Kong action film that has a similar fight scene to the final one between Smith and Neo in Revolutions, in that both take place in the skyline of a city during heavy rain, etc. Personally, this feels to me like more of a rip-off than an homage. Judge for yourself.

Crouching Tiger, Hidden Dragon - If you have seen Crouching Tiger, Hidden Dragon, pay attention to the fight between Neo and Seraph, the Oracle's Chinese bodyguard. It has the same exact hits, shots and music of the first fight of CTHD (it is especially obvious when we see both men's legs almost dancing rather than fighting). As the fight choreographer for both films is Yuen Wo-Ping, this may be a tribute to him from the directors.

Baraka - The Architect shows Neo images of the humans that will die if Neo chooses not to go into the right door. Many of those images are from the movie Baraka. A study of comparative religion, Baraka contrasts the purity and beauty of nature and religion with the ugliness and misery of modern technological society. Interestingly, some of the images that Neo sees are of people who were killed in Nazi and Pol Pot concentration camps, as Baraka seems to suggest.