Hello,
Most of the time, J2EE development uses Eclipse based development tools. As there are some difference between each editors, Oracle, IBM, myEclipseIDE and so on, the best thing to do first is taking the Eclipse from their site and take the JEE package (With WTP, Web Tool Platform plugin) which is totally free. You can adapt then to use the other one as needed.
As JEE server you can start with Tomcat but if you want a full JEE compliant server, you can have a look to :
- Geronimo
- BEA WebLogic (part of Oracle now, and free for R&D purposes)
- JBoss
As Tomcat is only the Servlet / JSP container, it does not support JMS, EJB and so on.
Another good alternative is to take the Sun NetBeans IDE and it comes directly with Sun GlassFish application server. Even the Sun's IDE is good and professional, I never used it in enterprise environments (always Eclipse based IDE) but very good for self-training.
Today, in enterprise development as well as in Open source development the Spring framework is commonly used. It would be a good advantage for you to know that framework which use the concepts of dependency injection and aspect oriented programming.
Hope this will help you and good luck
Cheers