If you have the source code for the application, you can compile it under Linux and have it run. You may also need to configure the locations where the application looks for things and expects to write to, but these details are typcially handled in the makefile and/or the configure script.
If you don't have the source (and you can't obtain it), you may still be able to run the application if you have the iBCS2 module available (or can obtain it).
Hope this helps.