Certainly /etc, and possibly /usr/local if you compile much yourself.
The greatest backup program in the world is free from sourceforge, and it is absolutely brilliant.
http://backuppc.sourceforge.net and download away. It allows you to backup through tar, rsyncd, ssh+rsync, and samba if you need it. I backup our entire company's servers through rsyncd, and the guy before me did it with rsync+ssh, all with backuppc.
Peace,
JimBass