I assume, that you're only new to web apps and not to Java itself.
For a starter, I can recommend the Apache Wicket framework for the front end. Their web site is full of examples, the mailing lists are a great place to get started, and Wicket in Action was an enjoyable read.
If you want to work with Java Server Pages (JSP), then you should definitely also include Java Server Faces (JSF) which make working with JSPs a lot easier. I can't advocate any good books to you as I went for web tutorials mainly. You might want to have a look at Apache MyFaces.
For the business logik, I guess the standard is Enterprise JavaBeans (EJB). I liked Mastering Enterprise JavaBeans 3.0. An older version of the book is available for free at TheServerSide.com. You should avoid EJB versions older than 3.0, because they are a PITA!
A separate part of the EJB 3.0 specification is the Java Persistence API 1.0 (see, e.g., Apache OpenJPA though the documentation is patchy). Other frameworks that support JPA are, e.g., Spring or JPOX (now being called DataNucleus).
Finally, if you want an application server for testing, there are JBoss by RedHat, SUN's Glassfish and Apache Geronimo (I preferred the last one, but you may have noticed my preference for Apache projects already ;-))
Good luck!