"Dragula", when Neo meets Trinity at the night club - in background as Trinity says "Hello Neo...".
"Mindfields", in the same scene - in background, faded into from "Dragula" just as Trinity says "My name is Trinity."
"Leave You Far Behind" (Lunatics Roller Coaster Mix)", during the fight training scene between Neo and Morpheus.
"Clubbed to Death", when Neo and Morpheus are in the "Woman in the red dress" program.
"Prime Audio Soup", when the crew of the Nebuchadnezzar are seen plugging into the Matrix for the first time with Neo in preparation for their visit with The Oracle.
"Spybreak!", during the lobby shootout scene.
"Wake Up", when Neo hangs up the phone at the end of the movie and flies away, continues into credits.
"Rock is Dead", credits.
Tracks missing from the OST
The music playing on Neo's headphones ("Dissolved Girl" by Massive Attack) when he is contacted by Trinity.
"Plasticity" by Plastikman aka Richie Hawtin, when Neo meets Trinity at the night club.
The background music when Neo fights Morpheus in the sparring program (Don Davis' "Bow Whisk Orchestra"[an anagram of "Wachowski Brothers"], combining semi-improvisational drumming, "Lunatic Calm's" mix of "Leave You Far Behind", and Davis' "Switch or Break Show" [also an anagram of "Wachowski Brothers"]. The version of "Leave you far behind" found in the soundtrack is the original album one, not the movie mix).
A track similar to "The Eyes of Truth" titled "The Conquest of Truth" composed and recorded by Paul Hanson for Music Junkies was used for the DVD main menu.
A track titled "(Can't You) Trip Like I Do", a collaboration between the groups Filter and The Crystal Method, was used for the theatrical trailer of the movie. This track can be found on the Spawn soundtrack album.