Are you planning an in-place upgrade of Windows 2003 or a re-install?
For an in-place upgrade I'm not sure whether you will run into any issues with the CRM installation. For a re-install, you will need to install CRM from new. During installation create a new organization (this will be deleted later). Once CRM is installed,
go to the Deployment Manager and import your existing organisation by pointing the wizard to the SQL Server and selecting the appropriate database. Make this organisation the default, disable the new organisation created during installation and then
delete it.
Also, check out this link regarding CRM on Windows 2008
http://support.microsoft.com/kb/950100