Personal observations based on the PDC WinFS release ...
1. Conspicuously absent from WinFS are WinFS object classes for infrastructure objects such server farm topology, server roles, X509 certificates, ACLs, NT domains, etc.
2. Conspicuously absent from WinFS are WinFS object classes for middle-tier application objects. For example, it would be interesting to see an entire MS application's traditional object model be represented as WinFS classes. Windows SharePoint Services's OM comes to mind as an excellent test case. Here's a small part of WSS OM we've modeled with Protege:
[A nearly complete WSS model can be found here]