In the highway chase scene, the license plate on Trinity's car says DA203. If you look in Daniel 2:3, which says "he said to them, 'I have had a dream that troubles me and I want to know what it means.'" This is possibly making reference to Neo's dream, because he went to the oracle partly to figure out what his dream about Trinity meant. The biblical text is speaking about King Nebuchadnezzar's searching for the meaning of his dream. In Verse 3, the Nebuchadnezzar says, "I have dreamed a dream." In Verse 5, when asked to explain his dream, he says, "The thing is gone from me" (all this is from the classic King James Version). Near the end of the movie as the Nebuchadnezzar explodes as a result of the sentinels' bomb, Morpheus says "I have dreamed a dream, and now that dream has gone from me."
Near the beginning of the film, Agent Smith drives up in an Audi with the license plate "IS 5416". This appears to be yet another Bible reference--Isaiah 54:16--reads as follows (from the King James Version): "Behold, I have created the SMITH that bloweth the coals in the fire, and that bringeth forth an instrument for his work; and I have created the waster to destroy." (Capitals are for emphasis).
The visual effects coordinator, who supervised the following shot, explained. Trinity falls out of the power station window, while firing at one agent, who dives out after her. He explained that the shot was done with Carrie Anne Moss sitting in a chair, with her legs stretched out in gynecologist stirrups. A camera on a track ran past and around her, shooting at high speed (so it could be slowed down to 24 fps). The sequence took over 200 shots to complete and was one of the longest non-CGI sequences of the film.
Towards the end of the movie when Trinity is actually going into the matrix on the motorcycle to help turn off the emergency power systems, it appears that the licence plate on her motorcycle said PS352. If you look in Psalms 35:2 (New International Version), it says, "Take up shield and buckler; arise and come to my aid." This could be alluding to how, though he doesn't know it, Neo needs Trinity's help in turning off the emergency power systems so he can reach the door that the keymaker is taking him to, that ultimately leads to the architect.
101 is also the number of the floor where the three have lunch with the crazy French dude.
Carrie-Anne Moss actually broke her leg during training for the Matrix Reloaded & Revolutions. Not wanting to miss out on working on the movie, she fell into denial about breaking it. She drove home and returned the next day before accepting treatment. By that time, her knee had swollen to twice the size. Even when out of action, she was present at training to give her colleagues encouragement. However Carrie-Anne got no sympathy from Keanu Reeves, saying "Everytime I sat down, he would call me lazy. He drove me crazy!".
When Neo, Trinity and Morpheus arrive at the Merovingian's restaurant, the camera pans left oddly from the main table to show a man walking away, looking over his shoulder at Neo. This man is the father of Seti from Revolutions. Kind of interesting, since in Revolutions, the father mentions his meeting with the Merovingian.
When Neo is meeting the Oracle, as well as when he's fighting the Agent Smiths right after, there are a bunch of words spray-painted on the fence, walls and bench, two of which are "one", spelled upside-down and backwards, and "role", which has to do with everyone having a role, or purpose, to play in and/or outside of the Matrix.
Anyone who was a big fan of the 60's TV show, The Prisoner, will see certain similarities between that and Neo's encounter with the architect. This is probably intentional since, in the first movie, an episode of the Prisoner (with Number 6 ever so appropriately meeting number 2) is playing in the background.