Using MySQL and Java? Check out an easier way: Yank
If you plan to create a Java Web Application which runs in Tomcat and accesses a MySQL database you'll need to add a Connector/J MySQL Connector Jar to the Tomcat installation. That's all you should really need for setting up Tomcat and Connector/J. Here's how to do that in detail assuming you already have Tomcat installed.
Step 1: Download the most current release of the Connector/J MySQL Connector from mysql.com and unpack the *.tar.gz file.
Step 2: Inside the unpacked folder you'll find a Jar called "mysql-connector-java-5.1.10-bin.jar" or something similar. Copy that file into Tomcat's "lib" directory.
Step 3: Restart Tomcat.
Piece of Cake!!