If you launch the DeviceEmulator by hand, those instances show up in the Device Emulator Manager in the "Others" node as GUIDs.  They aren't exactly user-friendly, but they are the most reliable way of uniquely identifying an emulator instance.

There are two things you can do to help identify running emulator instances:

  1. Right-click on a GUID in the Manager and pick "Bring To Front".  That will show you which emulator window corresponds to which GUID.
  2. When you launch the emulator, add one more command-line option, /vmname.  The string that follows the /vmname option will appear in the Manager in place of the GUID.  ie. "DeviceEmulator.exe xip.bin /vmname BarryPocketPC" will show up as Other/BarryPocketPC in the manager instead of Other/{...guid...}.

Barry