i'm running cocon on Jboss 4 with no problems. I have cocoon sitting in the following directory:
1. in /deploy/jbossweb-tomcat50.sar/root.war/
I removed everything that was in root.war and replaced it with my cocoon stuff. My setup is such that I do http://www.mysite.com/myfile.xml takes me to http://www.mysite.com:8080/myfile.xml
Thanks for the reply! Were you able to include the numerous Cocoon JARs successfully in root.war/WEB-INF/lib without crating conflicts?