What to learn for making Java web applications in Java EE 6?
Even if I know that this will be controversial, my advice would be to start with Java EE 6 only. So, grab GlassFish v3 and either get the book Beginning Java EE 6 Platform with GlassFish 3: From Novice to Professional or follow the Java EE 6 tutorial. In my opinion, the book (that I've started to read so I know what I'm talking about) provides more guidance which might be preferable if "everything" is new for you (it covers both the Java EE platform and its APIs and the environment to build, deploy your applications).
Now, as I said, I can already hear voices saying things like "Java EE is heavy, use Spring instead, learn Struts or Wicket or Stripes for the presentation layer, learn Hibernate for persistence, or not because I don't like ORM, use iBatis or straight JDBC instead (you'll see, it's cool with Spring, Spring is so cooool), and use Tomcat (and why not Jetty), or JBoss, or just forget all this and go for Grails, and bla bla bla...".
But I don't think that this is really helping you and, without mentoring or guidance (and you won't find a non outdated unique resource covering all combinations), this must sound very confusing for a beginner.
So, because I think that Java EE 6 is a big improvement over previous versions of Java EE, because it provides really nice standard APIs for all your needs (Servlet 3.0, JSF 2.0, JPA 2.0, EJB 3.1 lite, Bean Validation 1.0, CDI, etc), because these APIs are all more than decent, because there is nothing really wrong in learning them, because this is already a big task, because you have to start somewhere, I'd focus on Java EE 6 only and forget the other frameworks for now. More precisely, I'd start with the Java EE 6 Web Profile (and then add things if you want to go further).
By doing this, 1) you'll get started and you'll learn brand new things and 2) you'll give some time to all other frameworks and/or tools to adapt and prove that there is still a need for them. And if there is, it will still be time to experiment the survivors and you'll be able to understand much better why they exist.
My advice1 is to stop reading books and start implementing stuff. In my experience, book learning is poor a substitute for the knowledge you get by actually doing things.
Obviously ... you can come back and do some more reading later. And you will probably get more from the reading when you do.
1 - Context: this is advice to someone who has just finished reading two books on the topic, and is looking for more books to read. In practice you need to balance reading with doing.
Java EE 6 is really amazing. The only problem is that it's about 2 weeks old, and there is only 1 container currently offering it's features -- Glassfish.
I have nothing against Glassfish, I use it all over the place, several production instances, I love the product and the project.
That said, the details of Java EE 6 do not translate back to Java EE 5. Some do, many do, but the Web Profile, Servlet 3.0, the new Bean types, JPA 2, etc. Those aren't there.
So, by learning Java EE 6 first, you're simply constraining yourself to a single container. More are coming, but they're not here yet.
Tomcat, JBoss, OpenEJB, Glassfish, Jetty, Resin, Geronimo, etc. all work well with the Java EE 5 spec (at least those parts of the spec that they support, Tomcat doesn't have EJB for example).
I can't think of anything in Java EE 5 that wasn't carried forward to Java EE 6. Java EE 6 made some very old aspects optional, and those you simply wouldn't learn today anyway. Java EE 6 made some Java EE 5 stuff even easier (packaging notably, EJB Lite for example).
Learn Java EE 5 now so that you can actually apply what you learn in a variety of environments, rather that learning Java EE 6 now and discovering you may not be able to use much of what you learn.
No single book will teach you what you need to know. Servlets, for example, are a nice foundation, but for anything larger than a couple of pages or endpoint, you will want to use one of the many 3rd party frameworks, or JSF, and no book covers the core and then a framework on top of that.
The Java EE 5 tutorial is good at getting the foundations down, my major complaint is that they don't show you the source code. Rather they expect you to just download and run it. It's not discussed in the tutorial. I've found the Head First books to be pretty good.
For web programming, raw Servlets are important enough just to understand the request/response cycle but you don't need a deep understanding to make a leap to a 3rd party framework.
I'm a big fan of Stripes for an Action framework (vs a component framework), and the single Stripes book available is excellent (making choosing that an easy choice).
I can't suggest a Component framework book, and I actually would not recommend one right off. The component frameworks truly bury the HTTP core request/response structures. They bury them for a reason, and they gain value BY burying them, but I believe to be effective you need to have a solid understanding of these concepts early on. That's why I don't suggest learning a Component framework first.
The JAX-RS REST framework, included in Java EE 6, but readily installable in Java EE 5 or any servlet container, is excellent. Arguably it is what Servlet 3.0 should have been. But I don't know any books for that.