Setting up java heap space in windows is not a big deal. You just need to open a file named CATALINA and replace the old entries but if you guys have installed apache tomcat6 on windows 2003 using MSI installer then you are at a right place. Under given are few easy steps to do this task;
1. Open the installation folder of Apache Tomcat6.
(In My Case Its C:Program FilesApache Software FoundationTomcat 6.0)
2. Go to Bin Folder
3. Double click the EXE tomcat6w
4. Go to java tab and set you initial and default java heap space!!!!!!!