I have tried calling a native linux program with these (nautilus) and it consistently fails. Do I need a fully specified path (nautilus is in the search path mind you)?
I'd say that you're free to use a linux syscall to do whatever you want, including forking the process and exec'ing the linux program. That's the beauty of wine. You have win32 *and* linux APIs available at the same time.
Cheers, Kuba