Regarding the Windows port, it seems increasingly likely that we'll officially drop it. We've been working on this thing and moving it forward for the last 6 months, with testing and development only being done under Linux. The Win32 port is very broken now - Rice Video won't work for Win32, the GUI has totally changed and needs to be re-written, etc. I want to continue to focus on making this the best possible N64 emulator for Linux because it's the only one.
Unless a Win32 developer volunteers to refactor the Win32 GUI for the new architecture, fix all of the porting issues, and maintain the Win32 port going forward, then most likely Mupen64Plus will be unix-only.