At this point in time, Akeeba is tied to the Joomla! environment. That will start to change after the stable release of Akeeba 3.0. The initial plans are to support other CMS systems such as WordPress and Drupal. Nicholas has mentioned a plug in architecture that would allow other systems to be supported by writing a custom plugin for Akeeba.
The Pro license would allow you to purchase one copy and install it on all your Joomla! sites, so the Joomla! backups are easy. The Pro version also has the ability to specify external folder trees and databases to be included in the backup. This would allow you to back up your non-Joomla! sites. The restore process would have to be manual, there is no automated script that would restore only an added site.
I'm using a mixture of Core and Pro versions on my sites on HostGator.
Dale L. Brackin
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!
My time zone is EST (UTC -5) (click here to see my current time in Philadelphia, PA)