I decided to start using version control on /etc and ~/. I was talking to Sparty and he mentioned that he had been doing this for his ~/ directory. Sounded like a good idea.
A word of caution. Subversion (as well as others I assume), doesn’t preserve permissions. Upon reboot I had to chmod a few things to get back to normal. I did a quick google about preserving permissions but didn’t see anything in the requisite 4 minutes of searching. If you know of a way to do that please post a comment.
Overall though I am pretty pleased with the result. Now I can run etc-update with impunity!