rdiff-backup is basically a wrapper around rsync and ssh that by default mirrors a specified directory on the two machines, as well as providing incremental backups for files that have been modified.
Say I have a server and I just want to backup some directory (/etc) on that server to a directory on my desktop machine (/backup):
rdiff-backup firstname.lastname@example.org::/etc /backup/etc
Note that rdiff-backup must be installed on both machines, and that in this case, "root" is required on the server because some files in /etc will certainly only be readable by root.
Backups that are not automated tend to not happen reliably, so we must run this periodically in cron. However, in running the above command, there was a prompt for the root password on server.com, which will not work with cron.
We need to setup password-less authentication from desktop to server.com. Set this up using this guide: http://blog.langex.net/index.cgi/Admin/SSH-SSL/passwordless-ssh-authentication.html
Now add rdiff to crontab by executing "crontab -e" in a terminal, and adding the following line:
16 16 * * * rdiff-backup email@example.com::/etc /backup/etc && rdiff-backup --remove-older-than 6M /backup/etc
which will execute the backup from your desktop every day at 4:16pm, and then delete backups older then six months old.
See this excellent summary for more information. Honestly, if I had started using rdiff-backup rather then backuppc first, I might never have gotten around to trying backuppc.