I just finished porting an application from Windows into Linux.
I have to create an installer of the application.
The application is not open source         
        
I've also looked into this at work and I'd have to agree there really isn't a "best way". If your application is being distributed as source then I'd go with the make/configure methods packaged up in a tar.gz. That seems fairly universal in the Linux world.
A good way to get an idea of what to do is to look at larger organziation and see how they distribute their binaries.