Mupen64 support added to the next version of mGalaxy.
If you want to benefit from it right now, just open 'Systems.xml' in mGalaxy 'Data' folder.
Find this block:
<System Type="Console">
<Name>Nintendo 64</Name>
<AppPath />
<RomPath />
<SnapPath />
<VidPath />
<Emu selected="0">
<Cmd id="0" name="1964 / 1964 UltraFast" value="-f -g "%path\%file%ext"" />
<Cmd id="1" name="Project 64 v1.6 [Script]" value="%path\%file%ext" />
<Cmd id="2" name="Project 64 v2.1 [Script]" value=""%path\%file%ext"" />
</Emu>
<Extensions>.n64,.z64,.zip</Extensions>
<Active>False</Active>
<Script>True</Script>
<Database>False</Database>
</System>
And replace it by this one:
<System Type="Console">
<Name>Nintendo 64</Name>
<AppPath />
<RomPath />
<SnapPath />
<VidPath />
<Emu selected="0">
<Cmd id="0" name="1964 / 1964 UltraFast" value="-f -g "%path\%file%ext"" />
<Cmd id="1" name="Mupen64" value="-g "%path\%file%ext" -nogui -f"/>
<Cmd id="2" name="Project 64 v1.6 [Script]" value="%path\%file%ext" />
<Cmd id="3" name="Project 64 v2.1 [Script]" value=""%path\%file%ext"" />
</Emu>
<Extensions>.n64,.z64,.zip</Extensions>
<Active>False</Active>
<Script>True</Script>
<Database>False</Database>
</System>
There's already a FBA support. This system is named 'Multi-system [FB Alpha]'. Have you checked it?