Desktop file installed by =app-emulation/mupen64plus-1.5-r1 references program icon like that: Icon=mupen64plus-large.xpm But there's no such file in /usr/share/pixmaps and that means menu entry for mupen64plus displays no icon. In fact, that directory contains file 'mupen64plus.png'. Either the desktop file should be modified to reference the correct file or ebuild to install required icon file.
He probably copied http://git.debian.org/?p=collab-maint/mupen64plus.git;a=blob;f=debian/patches/fix-desktop-file.patch;h=5c21443ee3629640255c3011b5b1b70fb775c0b0;hb=eb71db70cd0471418e0edc50ba853ec20cc1db3f and doesn't supply http://git.debian.org/?p=collab-maint/mupen64plus.git;a=blob;f=debian/mupen64plus-large.xpm;h=645d293003639e5b2bc0ef818def948eebd95d53;hb=eb71db70cd0471418e0edc50ba853ec20cc1db3f - they use these things for their cross-desktop menu-system http://www.debian.org/doc/packaging-manuals/menu.html/ .
I fixed it without a bump. It's to much of a hassle to ramp the revision for this glitch.