There is a sub-group of version control users (a growing group, I believe) that manage their entire home directory in a version control system. There are several arguments for this use, and I have played with it off and on, but never really "moved in" all the way. I'm probably getting closer to the day.
Other people use version control for their /etc directory on Linux boxes. /etc holds much of the common configuration files on many Unix based distributions, and being able to "go back" to a previous configuration can be really handy.