How We Compile
https://github.com/punesemu/puNESSource Code For Windows ?
It appears to be the source code for both Windows and Linux versions.
If you click on Source/Gui/
There are folders for both 'Windows' and 'Linux'
You probably need to build it with MingW, since it appears to rely on AutoMake.
FHorse recently posted up to date WIP builds in his thread:
FHorse wrote:
Linux32Linux64Win32 D3D9Win64 D3D9Win32 OpenGLWin64 OpenGLUpdated links for the new WIP. The linux version now need that nvidia-cg-toolkit is installed.
He's preparing the v099 release according to recent GitHub activity.