<p>I am coding a client-server application using Eclipse's RCP.
We are having trouble testing the interaction between the two sides
as they both contain a lot of GUI and provide no command-line or other
remote API.</p>

<p>Got any ideas?</p>

I have about 1.5 years worth of experience with the RCP framework, I really liked it. We simply JUnit for testing...
It's sort of cliche to say, but if it's not easy to test, maybe the design needs some refactoring?
Java and the RCP framework provide great facilities for keeping GUI code and logic code separate. We used the MVC pattern with the observer, observable constructs that are available in Java...
If you don't know about observer / observable construct that are in Java, I would HIGHLY recommend you take a look at this:
http://www.javaworld.com/javaworld/jw-10-1996/jw-10-howto.html
, you will use it all the time and your apps will be easier to test.