I just picked up the two-disc DVD for the Matrix Reloaded. I noticed something that I had never seen before. At the end of the movie, when Neo reaches into Trinity's chest and massages her heart to bring her back to life, you see an X-ray image of Neo's hand on her heart on the computer screen on the Nebuchadnezzar. After we had seen the movie the first time, we were going for the whole matrix-in-a-matrix theory, and this just seems to throw more credence to the idea.