Mupen64Plus with M64PY
A portable version of this would help immensely, especially if controller settings, savestates, etc could be carried over from distro to distro, as by default it installs everything in the distro's filesystem rather than /home

Hm, Mupen uses Python plugins and M64PY is a Python frontend, that makes things more difficult as I have trouble packing up some Python modules in a portable way!
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Finall! http://www.portablelinuxgames.org/?id=mupen64plus
M64PY won't be feasible for now, because of the Python issue; however things like wxMupen64Plus should be feasible
I didn't redirect the write directory; you can probably do that with the --datadir or --configdir parameters