Sure. Do you only want your OS X Server to provide file services? If you have Windows 2003 Active Directory in place, you can join your OS X Server using the Active Directory plugin in Applications -> Utilities -> Directory Access.
You'll need to make some specific alterations to your smb.conf file, to have the Samba service join to use AD kerberos authentication properly. AFP is a little more complex. You'll need to create Kerberos keytabs.