One of the most annoying and recurrent problem in deploying off-the-shelf  open source java application in JBoss is the log4j conflict.  For example I incurred in the problem trying to deploy JamWiki
Because JBoss provide his own version of the Log4J libraries, if you have in your application your log4j, there is usually a conflict.
There are ways of solve this problem, the simplest one is to remove Log4j from your application and use the JBoss one.
At  the first glance, this look as an ugly solution, but recently discovered a big value with it: if you use the JBoss provided log4j, the configuration is reloadable without having to restart the application server or redeploy the application,
This is a great advantage when you debug your application (I LOVE debug by logging). Instead of having all sort of debug enabled, just in case you miss some important informations, when running on JBoss you can safely turn off everything, or just enable what you consider always useful.
When you approach a buggy section, you can enable on-the-fly the debug log you need, just editing the log4j.xml file. And of course you can also easily create new appender, in order to save in a file some relevant detail of your application.
I fell in love with this idea so much that this is the main reason I will use JBoss instead of plain Tomcat (as I used to do in the past) in my future development.