I don’t really like the way Multicraft handles backups. If you’re using a non-official server such as Bukkit or Spigot, and use a plugin that allows you to have multiple worlds (such as Multiverse), then Multicraft can’t handle backups of those worlds. Additionally, even if you allow Multicraft to backup all your Minecraft servers, those backups are still sitting in the individual server directories.
So, I wrote a script that pulls the list of servers via the Multicraft API, then proceeds to tar up the entire server directory for each server. Then, it uploads those backups to an rsync server. This is a much better backup solution as if anything were to happen with the server, such as a hard drive dying, then your worlds are gone.
Note that this script assumes that all Minecraft servers for a given Multicraft installation is on the server in which the script is running. This script will need to be modified to support multiple physical servers if used on an installation with more than one physical server.