I can't remember anything being too problematic. However, you should make sure to check for any specific WebSphere coding - I have a vague recollection this might be relate to any specific DB2 rapid development features. There may also be some JSP constructs that Tomcat/Jetty can't handle such as deeply nested expressions - e.g. An expression that should be evaluated that is within an HTML attribute.
You will also need to generate JBoss specific deployment descriptors to carry out any specific mappings. These will replace the special WebSphere deployment descriptors. The standard J2EE deployment descriptors should be able to remain intact - ejb-jar.xml, web.xml, etc.
Have a look at http://www.amitysolutions.com.au/documents/JBossJNDI-technote.pdf to see some explanation of descriptor changes and the reasons. There are also some other non-JNDI related additions such as for CMP and for web context. The forums and the paid for documentation cover these as well as the resource mapping.
Hope that gives you a start.
Most likely, you will have built some Struts based workflows using the WSAD tool so you will probably need to deploy Struts in JBoss as well. This might be another stumbling block if you have any specific Struts configurations for each deployment. YMMV.
Thanks much for your help.