Java Frameworks Integration
Eclipse web site
My Java workspace (Part 2) 
Web Container 

As web container, I use the most well known Tomcat, it is well integrated in Eclipse. Other can be used also such as Jetty, Resin... As I use Spring I never had the need to use an Application Server  such as JBoss, JRun, WebLogic, WebSphere... or the functionality related to them.
EJB Container
I never used EJB Container except for my own learning study. An EJB container manages EJBs and provides an easy way to access them via RMI. As my applications are based on Spring, WebServices, Hibernate, I don't need to use EJB.
I use SVN (SubVersion) as versioning system, it is easy to install and it is integrated with a lot of other product. A plugin exists for Eclipse.
Bug tracking 
As Bug tracking tools, I suggest to use JIRA. JIRA and SVN are integrated, you can track a defect and link this defect with a version of your code in SVN just by adding a comment while you check-in your code.
Building tool 
To build my application or any package of my application, I use Maven. Maven helps you to manage your dependencies and their version. It also helps you to deploy your package in a sharable repository and then each developers can retreive a given package version from this repository.