My Mupen64 installation is nowhere to be found in unity and unity2d as well... It works if I open it from terminal, but the gui is gone!
I see that after one month, you still not get good answer. So I try my "poor" answer.
I had the exact same problem than you. After installing Oneiric and install Mupen64, now no more problem, my Mupen64 icon is back in the Unity Dash.