Hello David, Welcome to Javaranch. I have seen many examples of Glassfish with Netbeans on web, which make me think that something new is coming.
I am using Tomcat most of the time with great success. Do you think it will be smooth transition to glassfish (if we like it)? I know app server market is crowed but it will nice if you can outline in two-three lines the greatness of glassfish.
I have used Netbeans and Eclipse both with great success so it won't be difficult to use your book, transition to glassfish and Netbeans. (current setup tomcat --> eclipse and GWT)
The reason you see a lot of examples using NetBeans and deploying to GlassFish, is because both are Sun products, most GlassFish tutorials are written by Sun employees, and Sun understandably wants to promote their own products.
However, there is nothing forcing you to use Netbeans in order to write code to be deployed to GlassFish. You can write code using your favorite IDE, there is a GlassFish plugin for Eclipse, and GlassFish is supported "out of the box" in Idea and (of course) NetBeans.
Additionally, the examples in the book are IDE agnostic, you should be able to load the code in any IDE and it should work just fine.
The transition to GlassFish from Tomcat should be smooth. As a matter of fact GlassFish uses (a slightly modified version of) Tomcat as it's own servlet engine.
Regarding "the greatness of GlassFish"
It is the reference implementation for Java EE, therefore it gets implementations for the latest standards before any other application server.
Being the reference implementation, it will always be 100% compliant with the latest Java EE specification.