The only time i make "File system Backups" is when i alter the files themselves or update vBulletin.
I take daily MYSQL backups through SSH and download to my computer. You should never store backups on your server it self. Because if a hacker gains entry into your server they automatically have an SQL dump to release to other sites. I also encode my Config.php with IONCUBE so if a hacker gets into my FTP all they can do is delete files and not access my SQL databases.
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