1. You could try MyEclipse (you have to buy a license) or RedHat Dev Studio (free) or look at eclipse-plugins.2y.net or at
www.eclipseplugincentral.com for plugins.
2. It depends what exactly you want your projects to do, but I would say, in most small / middle sized projects you won't need JNDI, JMS, WebServices, XSL ...
3. I don't know EJB, but hibernate, and it is really easy to understand and use. It may be an asset to understand EJB, but you can do with hibernate only as well.
regards, Manuel