Unfortunately, the Java EE space is so freaking astronomically huge that I think any one place isn't going to get you very far. I attempted to learn the Java EE stack via the Sun tutorial and I found that by the end of it I suffered from information overload. It's an incredibly complex space, of course, but at the same time I found that the tutorial was needlessly obtuse.
That said, I'm a fairly green developer with no real experience in the web app world (and honestly very little experience in the desktop world either) so I may have just not had quite enough brain power to grok. If you're more experienced, it is a great place to learn about the Sun technology stack (which, of course, is the other problem with the Java Web Space, there are way to many options).
A perhaps better approach might be to wait till you have an actual project, and then learn Java web development by doing. And the most important thing to remember is to not become afflicted by analysis paralysis. As the Java Posse said in a recent episode, you can really get away with Googling for a toolset or framework for your problem, go with the top 3, spend five minutes analyzing them, and then pick one and be reasonably sure that you've picked something that will meet your needs.
All that being said, I'll throw a +1 in for Enterprise JavaBeans 3.0 as an intro to EJB Session and Message Beans as well as the JPA. I have briefly looked at Core Java Server Faces, 2nd Ed. and was impressed by what I saw. However, again, also be aware that things like Hibernate are available for your persistence layer and have garnered, in some cases, much higher reviews than the JPA. Patterns of Enterprise Application Architecture did more for my understanding of actual Enterprise architecture than any other book I've read, although when you're using a tool-set, most of the patterns have been implemented for you already (but it might help your understanding of how to use them properly).