Flynn is intended to manage and containerize backing services as well. We'll have a system for specifying hosts and volumes that can be used for persistent storage. In the future we also want to add hooks for provisioning, high availability, and more.
Flynn apps are docker containers under the hood, so any docker container can be used to extend your Flynn deployment - including databases and pretty much any long-lived service you can think of. Take a look for http://index.docker.io for examples.
