ModeShape repositories can be used in a variety of applications. One of the more obvious use cases for a metadata repository is in provisioning and management, where it's critical to understand and keep track of the metadata for models, database, services, components, applications, clusters, machines, and other systems used in an enterprise. Governance takes that a step farther, by also tracking the policies and expectations against which performance of the systems described by the repository can be verified. In these cases, a repository is an excellent mechanism for managing this complex and highly-varied information.
But these large and complex use cases aren't the only way to use a ModeShape repository. You could use an embedded ModeShape repository to manage configuration information for an application, or you could use ModeShape just to provide a JCR interface on top of a few non-JCR systems.
The point is that ModeShape can be used in many different ways, ranging from the very tiny embedded repository to a large and distributed enterprise-grade repository. The choice is yours.