JBoss is J2EE specification compliant, it supports J2EE specification very well, such as EJB, JTA,JMS, JNDI and etc. Tomcat is only a servlet container, although it also supports a bit J2ee specification. When you want to use J2EE component, you should consider JBoss first.
Forgot a point, JBoss supports JMX very well, especially in version 4.*. I have experienced a project, it doesn't have a web UI, JBoss is used just as a platform and EJB container to integrate all the standalone application on it use MBean.
