I tried putting the jdom.jar that comes with JBoss 3.2.0 in the topmost lib directory of JBoss 3.0.6 and the server started without any errors during the bootstrap process. Does that work for you? I can't guarantee that it will solve any problems in use.
Also, the 3.2.x release already includes jdom.jar in the topmost lib directory ... if that is an option for you.
the jdom.jar contains a META-INF/info.xml for which JBoss can't find an appropriate deployer. This behaviour of the deployer is fixed in later versions of JBoss, if you want to stay with 3.0.4 you can simply remove the info.xml file form jdom.jar.