Make a flat Universe that you expose to the world.
Even when I use SOAP, which can easily handle hierarchical object graphs up to whatever depth, I flatten the graph and link everything with simple IDs (you could even use your database IDs, although the idea is that you want you don't want to expose your PKs to the world).
Your object universe inside your app is not necessarily the same one you expose to the world. Let A have children and let B have children, but there's no need to reflect that in the REST request URLs.
Why flatten? Because then you can do things like fetch the objects later by ID, or send them in bursts (both the same case, more or less)... And better than all that, the request URIs don't change when the object hierarchy changes (object 37252 is always the same, even when it's been reclassed).
Edit: Well, you asked for it... Here's the architecture I ended up using:
package: server - contains the superclasses that are shared between the front-end server and the back-end server
package: frontEndServer - contains a Server interface which the front-end server must adhere to. The interface is nice because if you decide to change from SOAP to a straight Web client (that uses JSON or whatever, as well), you've got the interface all laid out. It also contains all the implementations for the frontEnd classes that will be tossed to the client, and all the logic for the interaction between classes except how to talk to the client.
package: backEndServer - contains a Server interface which the back-end server will adhere to. An example of a Server implementation would be one that talks to a MySql DB or one that talks to an XML DB, but the Server interface is neutral. This package also contains all the classes that the implementations of the Server interface use to get work done, and all the logic for the backend except for persistence.
then you have implementation packages for each of these... which include stuff like how to persist for the backend and how to talk to the client for the front end. The front-end implementation package might know, for instance, that a user has logged in, whereas the frontEndServer just knows that it has to implement methods for creating users and logging in.
After beginning to write this up I realize that it would take a while more to describe everything, but here you have the gist of it.