There is an entry in the FAQ about backups, click here -> backup moodle
Personally I do as it suggests for mysql, but for the data I do something like...
zip -r /mnt/backup/mdbackup.zip /var/www/moodledata
where /mnt/backup is an offsite nfs mounted partition and /var/www/moodledata is the root of my moodledata folders. This script (along with the database backup) commands is run by cron daily. You could just put the whole script in /etc/cron.daily.
Exactly how you work this out rather depends on your setup and your existing backup provision (if you have one yet).
Installing and upgrading help
Adding drive space
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