I tried the Backupwordpress plugin on a few of my blogs. My main domain is the 'domain' and all the other domains are subdirectory/addon domains.
When Backupwordpress ran and backed up the main domain,I thought it would just backup my 'wordpress files', but it backed up EVERYTHING!
My host shut me down until I could contact them and figure out why a backup was being run every 7 days of my entire site of almost 5GB (against the terms).
If you have a similar domain setup using addon domains be very careful about using this plugin!
I would have posted this in the plugin owners forum or contacted him directly, but there is no contact form and his forum registration doesn't work.