When your device is synchronised with ActiveSync (or Windows Mobile Device Center in Windows Vista) a number of device properties are written to the registry. This allows you to gather information on the device during a custom installation or from a desktop application. One of these properties is the version number of the device, the exact key is:-
HKEY_CURRENT_USER\Software\Microsoft\Windows CE Services
The version is stored in a DWORD value called "DeviceVersion", its contents look like this:-
0x1560105
As raw bytes it would be {0x5, 0x1, 0x56, 0x1 }. The first byte represents the major version number, the second is the minor version and the last two bytes together are the build number e.g. 0x156 = 342. Putting that all together shows that my connected device is returning version:
5.1.342
Which is exactly what I can see on the Settings > System > About screen for the device (which is a Pocket PC running Windows Mobile 5.0 AKU 3.0).