When using ProjectGen to create a template, the third screen "Specify Project Properties" lists references that will be included with the template and allows you to add or remove references.  The catch is to add a reference, you need to know where the assembly is located and navigate to it (unlike in a project where you can select a reference from a list).  Unfortunately, you cannot simply navigate to the GAC and select the assembly from there.  If you are not sure where an assembly is located, try adding it to a project, then select the reference in the Solution Explorer and check out its Properties.  There is a Path property that will show you were the assembly is located.