Hi Kent and J.
To address Kent's original question, I'd say that there are two main dependencies that the book has on NetBeans.
First, the book shows how to set up NetBeans to work with
Tomcat and MySQL. There will definitely be some differences in setting up Eclipse to work with Tomcat and MySQL. But, once you figure out how to use Eclipse to deploy and run a servlet/JSP application on Tomcat, there shouldn't be many issues after that.
Second, the source code for the book is stored in NetBeans projects. As a result, to use Eclipse, someone would need to convert all of the source code for the book from NetBeans to Eclipse. I have done this before, and I haven't found an easy way to do it, so I'd say it's a tedious and time-consuming task. For now, I don't have any plans to convert the source code from NetBeans to Eclipse, but if I hear from enough readers like you who would like that, then I may. In the meantime, I recommend using NetBeans with this book, mainly because it's easy to open and work with all of the source code for this book.
I see Kent's point that he'd like to stick with Eclipse since that's what he typically uses. I also agree with J.'s point that it's good to not get locked in to one tool, and I think his summary of the pros and cons of Eclipse and NetBeans is spot on. I chose NetBeans for this book mainly because I agree with J. that it's easier to set up and harder to screw things up.