Great post with lots of good advice. I am already doing many of those things all be it in slightly different ways. In particular with regard to configuration files, I have started to suffix my live configuration files with .local so that I can have a generic exclude rule for *.local.

Don't forget, you really can put "everything" in source control. This includes shell scripts, linux shell configuration files, apache config files, the php.ini file, everything. If your repository is public, just be careful what you put in there so you don't give away the keys to the kingdom!