You might also want to think about files and directories in your ~/ directory (home). .gnupg, .opera, .mozilla, .bashrc -- these are things you probably want to have backed up. Maybe you have a bunch of scripts for Nautilus, so save .gnome2/nautilus-scripts, too.
What about your mail directories? Maybe you use Gringotts and keep your grg file in the .gringotts directory. Keep sharp about your hidden /home/you files and directories. Every once in a while burn them to a disc, label it, and file it away.
If you're setting up and running a server you already know the configuration files to back up, hell, just tar /etc and call it a day
With so many easy and reliable backup solutions you may wonder why I recommend having a working copy of typical system files around. Well, they can be handy, and not bad to have when you're rebuilding your system from scratch either.
Being able to do: mv /etc/fstab /etc/fstab.old, cp /home/you/systemfiles/fstab /etc/ is pretty nice.
For a quick restore using files instead of an image or similar I have on hand:
After I reinstall Debian I just rename the existing versions and cp my versions in their place, et voila! 'Course, I gotta make the directories in the /mnt directory.