well there are a dozen different ways to bacup anything... depends what you want to do really. the most effective way is normally to use rsync to maintain an exact clone of /etc. see the rsync howto to setup up a connection with a remote server.
at a more simple level, you can easy tar up /etc and place it wherever you see fit (possbily on a samba / nfs share on a remote machine)
Code:
tar -cjvf /mnt/backups/etc-$(date +%F).tar.bz2 /etc/
this should create a dated file in /mnt/backup of /etc/
i wouldn't restrict yourself to *.conf files btw... there's loads of config files that don't fit into that. /etc/fstab etc...