During configuration, it would be nice to acquire objects from JNDI and use the returned objects as properties on other configured objects (e.g. in INI config).
There is a JndiRealmFactory that already supports looking up entire Realms from JNDI, but it is more likely that lower-level objects would be acquired from JNDI instead (e.g. DataSources) and the Realms would be configured in INI and use those objects.
This would be pretty easy to support: there is already a Shiro Factory interface and an AbstractFactory class. A new JndiObjectFactory subclass could be created that uses a JndiLocator to look up and acquire objects.
The ReflectionBuilder implementation would need to be changed to handle encountering Factory objects - if an object in configuration specifies a Factory as a property, the builder needs to call the factory's getInstance method instead of using the Factory directly. I think this could be done in the ReflectionBuilder#resolveReference method without touching any other code.