Is there a difference? If you have a .NET app that runs under Linux, is it not a Linux app? (same goes for any platform agnostic runtime - java, js, lua, python, ...) There aren't that many languages that are really system-dependant. Conversly, many "Linux apps" written in C/C++ will compile and run just fine under Haiku or Mingw - does that make them BeOS or Windows apps?

It seems that "(Linux|Windows|Mac|BeOS|whatever) app" doesn't have the same meaning today...