Depending on how you write the app, yes.  If you are using the "standard" libraries for an commandline app, the source code should compile and link on both Microsoft and Unix platforms. The "standard" libraries will translate down to the OS specific libraries.

If you call the OS specific libraries yourself then you have lost any portability.

Desktop: This usually has some type of GUI on the app. While the concepts are the same across most platforms, the UI libraries tend to be proprietary to the OS, short of using a framework that is supposed to be multi-platform.

Enterprise apps: This usually means databases and client apps or websites.  While the concepts will be cross-platform, the code tends to be tailored to the platform libraries you are using.