Besides the prominent theme of Neo being Christ and the parallels between the supporting characters, many other religious symbols are displayed throughout the movie.  Many are also very subtle or obscure and many analysts of the Matrix have made their own perceptions on the meanings.  And while the writers and directors of the movie, Andy and Larry Wachowski, explicitly said that there were some religious connections, it is up to the viewer to decide how far these interpretations should go.  Personally, when I watched the movie (several times) I did not see any of these subtleties - but is this because of my lack of Christian knowledge?  Or are people struggling to find religious symbols and make a connection, when in reality, the movie is just sci-fi action piece and people interpret it however they want?

The hull of their ship bears a plate reading "Mark III No. 11".  Mark 3:11 reads, "Whenever the unclean spirits saw him, they fell down before him and shouted, 'You are the Son of God!'"⁴.  This clip is in the movie for less then a second but has a strong religious impact and follows the theme of Neo as Christ.

"Jesus! What a mindjob! So you're here to save the world."⁵
- Cypher to Neo, when they first meet.

"Hallelujah!" is the response. "You're my saviour, man. My own personal Jesus Christ."⁵
- Computer Hacker to Mr. Anderson in the second scene of the Movie.

Neo and Trinity are shown making love beneath an arch. In religious iconography, being shown beneath                                                                           an arch is a traditional sign of divinity.⁹

Neo's own gift of prophecy is explainable by the fact that, like the Oracle (the Gnostic Sophia, or Holy Wisdom—the female Godhead), he comes from beyond the Matrix—that is, the world—and thus exists outside of time, much like God in St. Augustine's theology.⁹

Neo's name in the Matrix, before he is saved, is Thomas Anderson.- The name "Thomas" can be linked to "Doubting Thomas", in that Neo never really believed that he was The One. "Anderson" is a play on "Son of Man", where the 'Ander-' finds its origins in the New Testament Greek root 'andros' meaning man. Christ was often referred to as the "Son of Man". "Neo" means "new" (And that's exactly WHY Neo was there - to make things "new", to bring about a new world order). "Neo" Anderson = New Son of Man.³

At the end of the first movie and throughout the second and third, Neo is able to manipulate gravity and fly when he is within the Matrix.  Mark 16:19 – “So then, when the Lord Jesus had spoken to them, He was received up into heaven, and sat down at the right hand of God.”³  This concept of ascension and being able to fly into the heavens in the end of the Matrix is a direct relation to Jesus’s ascent into Heaven.

This quote is taken from Copeland’s Matrix page (Reference #3) and picks up on many things in the first scene alone which I hadn’t made any connection with being religious or prophesizing.

“And consider this dialogue when Choi and DeJour come to Neo's apartment (apartment #101, no less!). Italicized dialogue shows pertinent pieces of dialogue that forshadows what is to come: 
Neo: What? What the hell?... Follow the white rabbit?... (knock, knock) Who is it?
Choi: It's Choi.
Neo: Yeah. Yeah. You're two hours late.
Choi: I know, it's her fault.
Neo: Got the money?
Choi: Two grand. [$2000?  Perhaps relavant to Christ being 2000 years old?]
Neo: Hold on.
Choi: Hallelujah. You're my savior, man. My own personal Jesus Christ.
Neo: You get caught using that...
Choi: Yeah, I know. This never happened. You don't exist.
Neo: Right.
Choi: Something wrong, man? You look a little whiter than usual.
Neo: My computer, it... You ever have that feeling where you're not sure if you're awake or still dreaming?
Choi: Mm, all the time. It's called Mescaline. It's the only way to fly. Hey, it just sounds to me like you need to unplug, man. You know, get some R and R. What do you think, DuJour? Shall we take him with us?
DuJour: Definitely.
Neo: I can't, I have work tomorrow.
DuJour: Come on, It'll be fun. I promise.
Neo: Yeah, sure, I'll go.”