running .net applications

mono supports .net up to version 2 or 2.5. doubt there's anything out yet that supports 3.5.
anyhoo, i read that canonical is not bundling mono in future releases, so your program will not work in ubuntu.

Just to clarify the above, mono, which sort of implements the .net framework under linux *can* be used -- but you may need to modify your application to avoid using less common features of the .net runtime.

If, in the future, you are interested in building proper cross-platform applications, you may wish to look at languages such as C++ or python, using cross-platform toolkits such as wxWidgets. These are not specific to any vendor, so can run on each system quite reasonably/

From a practical perspective, depending upon the size of your program, it may be possible to simply port it across by changing the function calls to the external library (ie .net). The popular example is the .net application "tomboy", a note taking application, was written in c#, with the .net runtime as a dependency.
https://secure.wikimedia.org/wikipedia/en/wiki/Tomboy_%28software%29

 A second programmer took the tomboy code and independently modified it to work under c++, without the .net runtime -- this yielded significant performance increases, and reduced the size of the application considerably. This was accomplished in a few weeks,

https://secure.wikimedia.org/wikipedia/en/wiki/Gnote