The LabVIEW Application builder (for LabVIEW on Windows 2000/XP/Vista/etc) will only build applications that run on desktop versions of Windows (XP, etc). To target mobile/embedded Windows OSes you will need an addition module - either Touchpanel (for Windows CE / touchpanel displays) or Mobile (called PDA in older versions) for PocketPC / WindowsMobile.
Its worth knowing that both of these options have stricter licensing agreements than application builder so applications cannot be distributed to large numbers of users in the same way. For example, a LabVIEW Touchpanel application will require either NI Touchpanel hardware, or a "Deployment License" for 3rd party hardware, for every device you run the application on.
Shaun
