In every WAR and EAR, you need to provide vendor specific descriptors. But it's no problem to provide two descriptors. Each appserv will look at it's own.
To easy the writing of the DD's, you may think about using XDoclet (xdoclet.sourceforge.net). This tool allows you to provide the meta information (DD's are META-INF, aren't they?) in you Java code using the @ tags. XDoclet can extract this info and generate the WebSphere / JBoss / Orion DD's.
I have built and deployed an ear to JBoss. I had to include the jboss.xml for my EJBs and the jboss-web.xml for my WAR, but no other JBoss specific files AFAIK.
Now, I'm just about ready to try and deploy it on WebSphere. I'm very inexperienced with Websphere 5.0, but it is my understanding that I can just deploy the .ear, and Websphere will generate default war and ejb descriptors for me during the deployment process. Can anyone confirm or deny this?
One thing I noticed about JBoss (3.0.4,tomcat) on my journey from war + ejb to ear was this: hot deploying wars and ejbs separately after a build, assuring the exact same compiled code in each, caused the shared classes between the war and ejbs to somehow get out of sync. I had to bounce JBoss. But, this didn't happen when hot deploying my ear. Just thought that was interesting...