剛剛看到這一篇Common Language Runtime Overview。
As part of their metadata, all managed components carry information about the components and resources they were built against. The runtime uses this information to ensure that your component or application has the specified versions of everything it needs, which makes your code less likely to break because of some unmet dependency. Registration information and state data are no longer stored in the registry where they can be difficult to establish and maintain. Rather, information about the types you define (and their dependencies) is stored with the code as metadata, making the tasks of component replication and removal much less complicated.
在.NET Compact Framework目前是沒有關於Registry的API，不過要怎麼包在Meta Data裡面，這倒是一個有趣的問題。現在的作法還是用opennetcf裡面的OpenNETCF.Win32.RegistryKey對Registry做處理。
如果你有修改Pocket PC上Registry的需要，我推薦PHM Registry Edit。
現在我是用目前利用.NET Compact Framework開發的程式，不過Load Time還是太長，不知道是CLR的關係還是我寫的太鳥 XD