Integration Server is designed to exchange text-based data with other applications. Integration Server is not an application server. While you can instantiate objects in Java services, and pass them around within the server, there really aren’t any good mechanisms for sending and receiving Java objects to and from other environments (short of dropping down to a Java service and doing the work yourself).
Recent posts and announcements re: JBoss and its bundling with IS change the landscape a bit. You might do some research along those lines if you really need to be exchanging Java objects. But you may want to confirm first that you can’t do what you need by exchanging text documents–that may be the long-term desired path for a variety of reasons.