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I've just been looking around, and I found some interesting things about some of the numbers that pop up in the Matrix movies. I don't know how much of this stuff has already been pointed out, or how much of it is valid, but here goes:

1) This picture(courtesy of the "Ascertain the Fate of the One" thread":
http://www.animallogic.com/film/matrix/images/explode_photo1_main1.jpg
Does anyone else see a "6" on Smith's chest? Maybe this isn't the first time this happened... Remember Reloaded?

This is the sixth anomaly, right? So is this the sixth time the One destroyed Smith?

2) Room 101 in M1:
What's 101 in binary? 5. The fifth iteration of the matrix.
Also, this could be an Orwell reference. In his novel Nineteen-Eighty-Four, room 101 is a room in which people confront that which they most fear. What does Neo/Thomas Anderson fear/hate? Not being in control of his own destiny...right?
Finally, with universities, something like "Science 101" is the most basic course in that field. That's kind of what Thomas Anderson's matrix life was, a place for him to develop basic perceptions and thoughts that would later allow him to "free his mind".

3) Room 303 in M1:
Well, I'm not really sure what this is, but it is definitely a dominant number. 303 COULD be rewritten as 3x101, so perhaps it is representing a room 101 for the trinity of Neo, Morpheus and Trin. They all had some powerful experiences associated with this room (Thomas Anderson dies there, Trin is forced to flee it, and Morpheus... watches it).

4) The bald kid in M1:
Everyone is familiar with the whole "there is no spoon" thing, but I've heard that there are also 5 bent spoons on the kid's cloth(I think). He hands the sixth spoon, which is straight, to Neo. This could be another reference to this being the sixth time the One has emerged, which could also be a reason that Thomas could only bend the spoon partway and impermanently(though he does go to the Oracle's apartment in Reloaded, does he find a spoon then?).

Anyways, those are just a few of my observations and speculations. I really need to get some sleep.

This last one is great. Good job seeing that!