Ah, you can get the UUID from the guest this way (as I hoped) in Xen Server v6.x: Serial number of the BIOS. For a Windows guest, you can use WMI to query that either locally or remotely. I suspect this ID-as-BIOS-serial was only introduced in Xen Server v5.6.
For earlier versions, you can get the UUID from the guest by running the old client tools. For a Windows guest, the executable is xenstore_client.exe, run that with parameter of 'read vm'. The output of that is a string, and the part after the forward slash is the UUID. Note you could use PSEXEC to remotely execute xenstore_client.exe.