We don't use EAR deployment or EJBs but we did have a number of war files that worked fine under a standalone Tomcat installation. These war's required specific version of some classes.
To support this I changed a configuration attribute for the whole JBoss Tomcat installation that made it work more like a standalone version. We've not experienced any problems from do thing. I suspect it may not be making best use of the class repository.
For JBoss 3.2.2:
In jbossweb-tomcat41.sar/META-INF directory fine the jboss-service.xml attribute.
Add/change mbean attribute:
By default it is true.
Hope this helps.