Depends upon the program!
You may find that a lot of them will work - I do
Take a copy of the Programs folder under Windows so that you retain the start menu shortcuts, and that will expediate your experimenting. The odd thing might need it, Windows CE Entertainment Pack is a software app example. All your drivers and Patches will need to go back on the device. You can also backup important registry settings to be dumped back on the device after the 'event'.