Strictly speaking, his brain is descended from a population that crash-landed on the computer some two million years ago so it's an open question whether it's even part of the matrix.
6 == what comes short of divinity, i.e., humankind (the number of man)
666 == emphatic rejection of the influence of the divine in humankind's affairs
42 == 6 * 7, the product of interaction of the divine with humankind, being the most elevated object in creation -- the understanding of this interaction is the ultimate answer, Douglas Adams stumbled on it
> 666 == emphatic rejection of the influence of the divine in humankind's affairs
Not really related I suppose, but in Judaism 666 has exactly the opposite meaning. The three sizes represent: the number of days it took to create the world, the 6 cardinal directions (NSEWUD), and the numerical value of one of the letters of gods name.
So in other words 666 is a number that represents the creation of the world.