Setting up the development environment for Java EE 6 with Intellij Idea and Glassfish.

You would need four things mainly:

• Java EE SDK
• Integrated Development Environment
• Application Server
• Database

1. Java EE SDK

Select your appropriate one from this link and then install it after downloading.

2. Integrated Development Environment

Sun recommends NetBeans for EE 6 development. It's free for both commercial and non-commercial use. However, I'm suggesting you to use Intellij Idea, which is arguably the best IDE for software development.
Download Intellij from this link. You might download the free trial of the ultimate edition and then register it later. Install it after running and following the on-screen instructions. This link might be helpful.

3. Application Server

I suggest you configure two application servers for development and test each of them. Namely, Glassfish 3 and JBoss 7. You would get a better idea about servers them from these so question 1 and so question 2. The bottom line is, JBoss and Glassfish are the two most popular app server. Though JBoss is supposed to be fast, it lacks JEE6 spec support compared to Glassfish. So, for now, let's just stick to Glassfish.
I suggest you take some time and configure glassfish according to this guide.

4. Database

Postgresql or Mysql would be fine.
sudo apt-get install postgresql-9.1
sudo apt-get install mysql-server
 
That's all for now.