You should always backup your system since that is the only way to recover if something goes wrong.
The C3000 comes with a backup and restore tool which is located under the Settings tab. Use this application to backup your Zaurus. It allows you to backup your system (flash, applications and configurations) to either SD, CF or /hdd3. Basically, everything except /hdd3 will be backed up and can be restored which means you will need to backup /hdd3 by other means.
Since /hdd3 is quite large, you either need to get a big CF card, or mount a Samba or USB drive that has enough space to hold your data. A USB drive would be the best (cheaper than CF drive and faster than Samba since its connected directly and not over a network).
Assuming you have your USB disk mounted as /mnt/usbdisk1 you could do the following to backup /hdd3:
# tar cvf /mnt/usbdisk1/hdd3-backup.tar /hdd3
If you are paranoid you can backup /hdd1 and /hdd2 as well:
# tar cvf /mnt/usbdisk1/hdd1-backup.tar /hdd1 # tar cvf /mnt/usbdisk1/hdd2-backup.tar /hdd2 # tar cvf /mnt/usbdisk1/home-backup.tar /home
You should also compress the files.
# gzip /mnt/usbdisk1/hdd1-backup.tar # gzip /mnt/usbdisk1/hdd2-backup.tar # gzip /mnt/usbdisk1/hdd3-backup.tar # gzip /mnt/usbdisk1/home-backup.tar
I have written a script called hdbackup which will backup /hdd3 by archiving and compressing each directory separately and datestamping them so regular backups can be made by simply running a command.
Alternatively, you can connect your Zaurus to your Windows PC through the USB link cable and use Windows backup software or anything else you like to backup the USB drive that the Zaurus is recognised as. Since the USB PC connection is buggy, you might be better of enabling Samba over wireless or LAN and then backup /hdd3 over the network.