FCEUX is written for two platforms: SDL and Win32. The two ports have some significant differences. The Win32 port has an extensive set of native gui amenities and tools. The SDL port supports many of the features of the Win32 build (Lua scripting, movie recording), however some of the Win32 features are exclusive to the platform. The Win32 port has a built-in GUI, whereas the SDL port has a GTK launcher GUI. The SDL port should run any UNIX-like OS (Linux/Solaris/BSD).
Network play is not presently functional. Fixing it is a high priority.
The latest win32 interim build is generally fresh within a day or two. If you are working with a developer to fix an issue affecting you then this is where you will find your fixed build.