I have a program written with the standard Arduino IDE in C. Is there any way that I can port my program to C# so I can use it with .net and my Netduino?
With enough time, most certainly. You will probably run into problems when your Arduino C/C++ project uses AVR-specific hacks and options like timers and interrupts. From my understanding you can do these more advanced things on the Netduino but there is a significantly different way you'll have to go about coding it.
In order to effectively port the code you'll need a good understanding of C, a strong understanding of C#, as well as the Arduino and Netduino build process, coding conventions, APIs, etc.
The Netduino has absolutely nothing to do with an Arduino.
If there isn't a library which understands the Arduino library (like [digitalWrite()]), then you'll need to write those functions in whatever language the Netduino uses.
There's a rough correspondence, but it takes a lot of manual transcoding to port.
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