This may not address your particular needs but it might be worth considering.
I have been using Mercurial (a distributed revision control system) to:
1. backup user-entered data on my linode to my home PC
2. allow for revision control on system configuration files on the linode
3. allow for revision control on various programs I am developing on my linode and allow for simultaneous development and merging with versions of these that I am working with on my PC at home.
what I do is to place a directory tree under mercurial for revision control on the linode and add the files into revision control that I want to track with commands like:
hg init dirname
cd dirname
hg add filenames
hg commit -m "some message"
then on my PC I can clone the data from the linode with a command like:
hg clone
ssh://username@linode.ip.address//full/dir/path/dirname
You only need to do the clone once to get the initial copy happening. Once the clone is done you can modify, add, delete files on either your PC or your linode and then on the PC you can:
hg pull
to "pull" changes that have been commited on the linode into the PC's copy, and:
hg push
to "push" changes that have been made and committed on the PC back to the linode.
All of the communications happen over SSH (on the PC mercurial will use putty to do the actual SSH stuff). And if you make changes to the same files in both places mercurial (i.e. hg) will provide you with a merge tool to help sort out any conflicts.
If you only make changes at one end (such as user entry of data into a web site on your linode) then you will never hit a change conflict and you can just keep "hg pull" ing the data back to your PC to back it up.
In theory, if you ever need to blow away your linode and reinstall it, the process of restoring all this data should be pretty straight forward, just do a set of "hg clone" commands on your PC (where the backups are) and set the target as being the directory on your linode you want to recreate.
See
http://www.selenic.com/mercurial/wiki/ for more information on Mercurial, to get this installed on your debian linode its just:
apt-get install mercurial
The installation of mercurial on the PC is pretty easy too.
Regards,
Stephen