Let's keep things separate: C# is a programming language - it is NOT an IDE. The IDE used for programming the NetDuino is the same IDE used for programming .Net solutions for Windows and Web - it is called Visual Studio (VS). Using VS, you have a choice of languages, but for Netduino development the selection is limited to C# and Visual Basic (I think... but I haven't tried to use any other). Both languges are used also for Windows and Web development, and currently not all language features are available in the downscaled .Net Micro Framework which is used for NetDuino development.
-knut