System backups should be done as root.
[on Ubuntu 12.04] I do backups with rsnapshot, which is a Perl script that uses rsync. I back up these directories and exclude everything else:
/bin, /boot, /etc, /home, /lib, /lib64, /opt, /root, /sbin, /selinux, /srv, /ubiquity-apt-clone, /usr, /var
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