Although this post will likely be closed as it is not a real question and subject to opinions, I will none the less give my opinion for you.
I am learning Java EE myself using NetBeans and Glassfish using the Java EE Tutorial and Beginning Java EE 6 with GlassFish 3
For application Server: JBoss has alot of hosting options around, I haven't found as many for the other app servers.
If you are looking for libraries already supported, both JBoss and Glassfish conform to the Java EE 6 spec. Glassfish is the reference implementation for EE6.
Jboss favors Eclipse and Maven (among others) while Glassfish favors NetBeans and ANT (among others).
With that being said, I will finish by saying that any choice is dependent upon your goals, as well as your familiarity with the tool chain.