<p>Needs to be secure and able to handle thousands of users.</p>

Check out ADAM and AzMan.
ADAM is Active Directory Application Mode.  There is a how-to guide at:
http://msdn.microsoft.com/en-us/library/ms998331.aspx
AzMan is Authorization Manager.  There is a how-to guide at:
http://msdn.microsoft.com/en-us/library/ms998336.aspx