Well all our machines are linux and run cPanel so we make use of BMU which is a script someone made. It uses rsync to put it to a specific folder and from there archives it and sends it to a backup server via ftp. If I was not using cPanel probably just use rsync via cron every night.
We use Ahsay online that works on both O/S's The license is not the cheapest out there but its very easy to install and use.