Right, I've solved this now. For anyone with a similar issue, here is my understanding of the situation:
To recap, I'm trying to get a minimal JOGL example working in an Eclipse RCP application. The application compiles fine, but craps out at runtime with "java.lang.NoClassDefFoundError: javax/media/opengl/GLEventListener". This seems like typical classpath fun and games, so I fart around and set my CLASSPATH environment variable (I'm on Win XP) to include the world and his wife, but of course it still doesn't work. I try putting all the JOGL crap in the "\jdk1.6.0_01\jre\lib\ext" directory. This not only doesn't solve the problem, but now it won't even build (Eclipse complains about Access Restriction on the JOGL stuff; great) - I know putting the JOGL stuff in here is naughty but I'm just trying to get it to work, so w/e.
What I didn't realise is that Eclipse ignores the CLASSPATH variable, so messing around with that is a waste of time. My understanding was that if you included a JAR in the Project > Properties > Libraries > Add External Jars bit, then Eclipse would sort out the CLASSPATH stuff for you, and certainly it adds some stuff to its little .classpath file, but it doesn't work at runtime, so there you go.
Anyway, I think this is some special wierdness of making an RCP application. I think you have to do Other Things to get the CLASSPATH sorted for external JARs in an Eclipse RCP application. Here's what I did:
Start a clean RCP Plug-In project in Eclipse. Add a lib directory to it. Put the gluegen-rt.jar and jogl.jar in there. Right-click on them in Eclipse and do 'Add to Build Path'. Right-click your MANIFEST.MF file and do 'Open With' > 'Plug-in Manifest Editor'. In the Manifest Editor select the Runtime tab. On there, under the Classpath bit click 'Add...', and select your lib/gluegen-rt.jar and lib/jogl.jar. That's it really. This is basically following the steps here:
To see some JOGL stuff, add a View and if you use the code from here it should work:
Hope this is helpful to someone.