My preferences to develop J2EE Projects :
IDE : Eclipse + several plug ins (for you JBoss IDE to deploy, hot deploy and hot buil your application) or WTP.
The best tools I've seen is MyEclipse, a J2EE plugin (but under license) for eclipse witch contains very useful tools to develop, deploy, and test J2EE applications that containts JSP, Servlet, EJB's (generated with XDoclet).
Unit Test : JUnit + JUnit plugin for eclipse
Build Process Tool : Maven + MavenIDE for eclipse.
Continuous integration : CruiseControl
That my experience.