This morning I also spent considerable time scouring the web for pages that debated and explained the philosophy and theories behind the trilogy, some I've read before (esp. regarding The Matrix and Reloaded), and a lot of new ones (regarding Revolutions of course). I am especially interested with the amount of details that this people managed to catch and interpret such as the symbolisms of the inscriptions on walls, names of people and places, and the more seemingly trivial facts of rooms and floor numbers and the hidden meanings that they try to cull out of anything that is said in the whole trilogy.
Bits and pieces:
1. The name Morpheus comes from the Greek word "morphe," which means shape or form; the first Morpheus, the Greek god of sleep, has the ability to bring changes in dreams: shapes, forms, realities. There's no doubt that in The Matrix, Morpheus plays this role; he's the one who's supposed to wake everybody up. Source
2. Neo is the One, Smith is any-one (all agents have everybody's names like Smith, Jackson, Brown) Source
3. The cave of Zion is meant to represent Plato's Cave, all of its inhabitants living " in the dark". In roughly 400 b.c., the philosopher Plato postulated a scenario where people are born and live their entire lives imprisoned within a cave. The entrance to the cave is covered by a sheet of cloth, so that the only thing the cave inhabitants would ever perceive of the outside world would be passing 2D shadows of the external 3D reality. Hence truth a.k.a "real world" vs. the matrix. Source
4. After Cypher betrays his friends in the Matrix, he tells the agent that he wishes to come back as someone famous, an actor, he wants to be powerful, and he wants to remember nothing. Now, the agent calls Cypher Mr. Reagan, so Cypher could be Ronald Reagan. He was famous, an actor, was very powerful and since he has Alzheimers, he can't remember anything. Heheh.. this is funny (considered as an easter egg). Source
Check out the above sources and links below for more theories, explanations and other trivia:
In The Matrix Official site, click on the mainframe panel, on the square with the matrix 0302 (third place, second row), the philosophy link. There's list of papers exploring various philosophical and theological topics with regards to the trilogy.
A discussion (supposedly spoilers) written before the release of Revolutions - very intensive, highly recommended!
"The Matrix" and philosophy : An A to Z Guide
How Christian is The Matrix?
A Forum page for the Matrix afficianados
Also other theories before Revolutions came out
Archive of 'easter eggs' in the Matrix
There is a even a book written on this subject entitled The Matrix and Philosophy: Welcome to the Desert of the Real.
As Neo himself said. Whoa.