Yeah, Christ references are pretty obvious and prominent in the end scene. When Neo finishes off Agent Smith and the scene cuts back to the face made of sentinels, the "voice" says, "It is done."
This parallels Jesus's uttering, "It is finished," right before he dies, redeeming mankind in the book of John.
And there's other parallels like Neo's pose and the darkness over the whole land during this cruxificion scene of sorts.
-Al
The biblical references continue:
Thomas - name of the disciple who doubted Jesus' resurrection until confronted with the nail scarred reality. Source of the term "doubting Thomas" which would describe the hero in the first movie.
Anderson - means "Son of Man" a reference from the book of Daniel and one of the most commonly used names for the Messiah as used by the Messiah.
Trinity - three in one, refering to the fact of God being a three equal person unified deity (Father, Son, and Holy Spirit).
Zion - ancient term for the city of Jerusalem.
Cypher - the turncoat enemy from the first movie (like you could forget him) alludes to Lucifer, a common reference to Satan (as well as the King of Babylon, the planet Venus, and sulfur-headed matches).
Nebuchadnezzer - first ruler of the Neo-Babylonian Empire for 44 years who conquered Jerusalem in a series of three invasions, resulting in the utter destruction of the city and exile of the Jewish nation into Babylon.
Morpheus - no real name tie in (Morpheus was the Greek daimon of sleep) however, he was the Voice crying in the wilderness for Neo ala John the Baptist.