The jboss-web.xml file is empty because the typical information (conetxt) is not used. You can omit the file and the portlet still works fine.
The jboss-app.xml file simply supplies a nice app name for the portlet. Otherwise the app name ends up being something like "/iframe". But you will never notice this unless you look at the Instances list in the Administration Portlet.
The jboss-portlet.xml file is described in section 6.1.3 of the Reference Guide that comes with Portal 2.4. Uusually you don't need this file, and given the current contents, I think it can be omitted.