Sqlsyncup is a project mainly written in ..., it's free.
backup remote mysql databases with an easy-to-use directory structure
sqlsyncup http://github.com/c3w/sqlsyncup
This script requires a skeleton structure as follows (pardon my ascii directory tree) BACKUP_ROOT
[additional hosts, like above ] | + [sql database] | + [sql database]
The upshot of this is that you only need to create a directory to add it to the backup list.