A very good book to start with is the "Apache Tomcat Bible" from Eaves, Jones & Godfrey. It explains how to install the J2SDK, Tomcat, MySQL,
Ant and Eclipse. And it has the source code of a web application built following the guidelines of the Model-View-Controller design
pattern.
There's another must have : "core servlets and
Java Server Pages" from Marty Hall. You can buy the second edition, or you can download the first edition for free in pdf format at Marty Hall's website :
www.coreservlets.com.