At Absolute Software we have used Windows CE in many several projects, writing basic applications that are basically simple user interfaces to applications that control external devices.
The biggest advantage of using Windows CE is the ease with which it allows you to develop user interfaces in a matter of minutes, compared to a couple of weeks if you were developing for a normal embedded system. As an added bonus the overall look and feel of the application will be familiar to anyone who has used a Windows PC.
When developing applications for Windows CE there are two main routes that can be perused:
The Visual Studio .Net route
Using Visual Studio .Net is the easiest method of development for Windows CE and allows the use of the .Net Framework, making applications easily portable to different devices. The biggest disadvantage of this method is the lack of access to lower level hardware that may be present in the system meaning any specialist hardware you attach to the device cannot be used from within your program.
The eMbedded Visual C++ route
eMbedded Visual C++ is the other main route for Windows CE development. It is ideal for developing software for specialist hardware and as an added bonus the compiler is free to download from the Microsoft website. eMbedded Visual C++ does not support the .Net framework but it does support MFC (Microsoft Foundation Classes) to allow applications to be developed with ease.
Another great advantage to using Windows CE is the ease with which it connects to your Windows PC, simply installing Microsoft ActiveSync allows you to plug in your Windows CE device and access all of its files from the familiar Windows Explorer interface. If you require more control then you can write custom applications using the Remote Application Programmers Interface (RAPI), allowing you to access basic file management as well as starting and stopping processes on you Windows CE device.