UPDATE 1:
I have now setup IIS6 so .NET can handle calls to .css files. What do I have to do now to get it to change css files based on the referal
Based on the domain name, you can dynamically control the part of the page from the code behind (.vb or .cs files or even a class). This will give you control to replace the css file based on the domian name. Capture the domain name in the code and then replace the css file/link, infact the whole part in the code behind. you can do this in C# or in VB.