I have an application I wrote that is designed to run on a windows system but now starting to think I would rather be using Unix. Would the application have to be 100% rewritten to work on unix, or is there something I could install that would allow me to run my .NET application inside unix?
There is no way to do this. Microsoft .NET applications are not portable to unix platforms.
Have a look at mono... might be what you are looking for:
A while back I spent a bit of time rewriting some applications that were originally written in C#. I used mono execute the original code on test data to generate some benchmarks and expected results for verification. I don't remember having any issues, but my goal wasn't to use the C# for real either.