Which variant have you considered for SSO? NTLM or Kerberos?
I've managed to set up NTLM SSO with the passthru subsystem in Alfresco running on Win 2k8r2. However, since that requires NTLMv1 I decided to go with Kerberos instead. I never got that working in Windows, so instead I installed Alfresco on a Linux server (CentOS) and then everything works.
So, please let us know what your intentions are and how far you've gotten.