If you use Java, you should know that to take full advantage of it you need a container such as Tomcat, http://jakarta.apache.org/tomcat/index.html, with that having been said, you should also check the jakart project in general which has some really good packages that are very useful for Java web development. Such as Struts, if you want to go Model-View Controller, which is an application architecture in which there are three distinct parts, Model - the core business model, which is where are the logic and data are stored, some commercial applications refer to this as the DAO (Data Access Objects). Views - these are generally JSPs, but you can use servlets as well, I don't recommend this, because they are more complex than JSPs, especially with the addition of Struts to the fray. Controller - these are the filters, servlets that provide verification and other functionality such as this (redirection, filtering out traffic from an I.P. beginning in 12 or something). Your model consists of a bunch of java beans, which I'm sure was in another forum here. Views and Controllers can be done however you want. You can use the JDBC to connect to MySQL.

Some resources for you:

http://jakarta.apache.org - several java-based, or java-centric tools from the apache foundation
http://struts.apache.org - struts home page, notice also part of apache foundation.

http://resources.corejsp.com/ - jsp, java web devel resources,
http://www.freeprogrammingresources.com/jspbook.html - even more java web devel resources

Have fun, you can do a lot with Java web technologies, if you fully take advantage of them.

I think this was more of what you were looking for grom the start, so check these resources out, and let me know if you need any more.