Recently, I set up a intranet for our company, which running on Windows Server 2003, and web server is IIS 6.
We use Apache Tomcat to serve the dynamic request from user, like sales report.
There is a good link about how to link Tomcat 5.0 with IIS 6 on windows server 2003, which at http://tjworld.net/help/kb/0001_iis6-Tomcat5-JK2.html .