I've done something similar on my home server. Not nearly as much data, but enough that I didn't want to have an extensive backup:> Actually a few GB of MP3s for that Jukebox rpm, which are already on CDs so there is no point in backing them up again.
I didn't want to edit the actual backup script to say "skip these directories" as that gets too far into customization.
[this assumes you are using "backup to desktop" and know a little bit about linux]
The backup takes only the configuration information, user data, i-bay data, and several system files like /etc/passwd.
So, to get around it, I made a new directory off /, called /mp3 and then stored all my .mp3 files in there. I then made a customization to httpd.conf (templates-custom) to FollowSymlinks on ibays, created my mp3 ibay, symlinked the contents from /mp3, to the mp3 ibay, and therefore everything functioned as expected, and the backup will only backup the actual contents of the ibay (i.e. the symlinks themselves but not the .mp3 files in /mp3).
Cut my backup from ~4GB to ~300MB.
Regards,
Jay