By default JCR Values are stored in the Workspace Data container along with the JCR structure (i.e. Nodes and Properties). eXo JCR offers an additional option of storing JCR Values separately from Workspace Data container, which can be extremely helpful to keep Binary Large Objects (BLOBs) for example.

Value storage configuration is a part of Repository configuration, find more details there.

Tree-based storage is recommended for most of cases. If you run an application on Amazon EC2 - the S3 option may be interesting for architecture. Simple 'flat' storage is good in speed of creation/deletion of values, it might be a compromise for a small storages.