This is an interesting forum thread discussing the possible way that the Matrix trilogy MAY end up. He dubs it all as a big spoiler, but concidering it's all just conjecture at this point and he's just extrapolating what has been said and done in the first two movies, I don't really concider it a spoiler. It just gives you extra symbolism to look for and it would be interesting if everything in Revolutions DOES resolve itself like this guy has foretold.

The most interesting elements are:

Everyone is a machine that is in an EMP-pulse 'coma' and plugged into VR (like the robot in the last Animatrix short "To a machine, all reality is virtual reality."). This is also shown in the scene near the end of Reloaded where Neo knocks out the Squiddies with an EMP pulse and collapses himself.

The various Agents in the system, as well as the Twins, are actually former Ones that failed and were absorbed into the Matrix.

And lastly, The Matrix is the eventual result of all of Keanu's former movies rolled into one. (I'm not kidding! It's there at the bottom of the thread!).

There are some other neat points, but I'll let you read it yourself (you have to doubleclick on the text to highlight everything, or just do a Select All command to see it). Like I said, I don't really concider it a spoiler, so much as a possibility of how things could wrap as well as one interpretation of what has come before. Neat read though.