As long as you are careful to not assume anything about things like file system layout and use libraries that are also portable, there would be little problems for porting VS .NET projects to MonoDevelop.
And one thing to keep in mind, Mono doesn't have the entire .NET Framework stack available. Almost all of the BCL is intact, but libraries like WPF are not available on Mono. Mono recommends you use GTK# for your GUIs.