Although portage takes care of configuration files very well, no system can have enough protection from human errors. Versioning configuration files under /etc is a nice solution to this. If you do a mistake and delete some file or any other silliness that might happen , you just revert to a former revision and solve the problem.
This can be achieved very easily:
svnadmin create /root/svn
svn import /etc file:///root/svn -m 'Initial import'
rm -rf /etc
svn ci file:///root/svn/etc
Now change some configuration files and do 'svn status' When you change your configuration files you can commit them to the repository:
cd /etc svn ci -m 'Changed MAKEOPTS=j2 in /etc/make.conf'Linux rulez!