Cap'n
If you are looking for a serious answer I can refer you to both their explanations. Calpreps uses Freeman to do the math and I my opinion this mathmatically really represents a true linear algebraic approach to the problem because they feel it should be completely non subjective. To Epics point this is or can be a bad approach. In essence Calpreps uses no human input after I think week 4( they do take into account player graduation, returning players etc if the coaches respond to their request for information and/or otherwise guess).
Massey is a much more extreme treatment of data applying linear algrebra but then combining minimization techniques to account for anomaliestic behavior in the mathmatical solution which yield unexpected results as the season progresses. The mathmatical treatment of data for both systems is attached below. I use a lot of this crap daily in my work but it is still a lot of hand waving and assumptions in my opinion. From a mathmatical standpoint Massey is a friggin genius.
http://www.masseyratings.com/theory/massey97.pdf
http://calpreps.com/ratings.htm