To run Tomcat as is on Windows Server 2003, you had to run IIS 6.0 in IIS 5.0 Compability Mode which disables all the goodies IIS 6.0 brings to the table. Running Tomcat on another port has many downsides and replacing IIS 6.0 with Apache is not a choice either if you need to do ASP.NET tinkering as well as JSP and java servlet stuff like I do.
Behind the scene, neither Apache Foundation nor Microsoft seem to be interested in fixing the problem even though there are more Tomcats running on Windows platforms than any other platforms. That sucks for developers like me. So I started writing an ISAPI Extension a few months back that runs Tomcat in IIS 6.0 application pools. As it goes, a crash project dropped on my lap and I had to drop it after spending only a weekend on it.
Now it looks like there is a solution called JspISAPI. I can't touch my server just now, but I am going to give it a spin next weekend. It costs $50 bucks but that's far cheaper than my spending additional 20 hours needed to debug and test my ISAPI extension. Besides, I was planning to give mine away which would have left the authors of JspISAPI without much of a market. As a commercial developer, I want to support other commercial developers by buying their product instead of driving them into the ground to satisfy my hippie ideals.