If you're interested in writing an application using C #, do a small search for Compact Framework (CF). This is a stripped down version available in Windows CE.
Remember that Windows CE is a very customizable OS, and you have no guarantee that it will support a component of your application (including C #) - Windows Mobile (+ PocketPC, + SmartPhone2003) is a completely different story.
When developing for Windows CE, you need to use Visual Studio 2005/8 Professional to support Smart Device. When you develop C # applications using VS2008, you target CF3.5, and when you use 2005, you target CF 2.0
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