When Neo is in the office on the phone with Morpheus trying to escape, look at the pictures on the wall to the right of Neo's head, they look like they're objects covered with the Matrix Code, much like when Neo comes back to life and he looks at the agents, and we see the Matrix code.

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.

The film's premise was based on Plato's Dilemma of the Cave.

When Neo is fighting and falls in slow motion to a complete stop, and then the camera pans around him completely stationary in mid-air, he fell through a ring of SLR still cameras which were all triggered simultaneously.

The scene where the sentinels come for the first time is a large allusion to Star Wars: 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, sort of 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."

All of the main action inside the Matrix takes place at The Heart of the City Hotel. This is a metaphor on a couple of levels: Using the heart in the world of the mind (the Matrix) entails being in love (Trinity and Neo), which is what unltimately saves them. The second metaphor is tied to the first: The hotel is in the heart/center of the city (inside the Matrix), but the heart (the organ) is at the center of the story; love is needed to conquer the Matrix.