This is seriously bizarre. I thought it was odd that I was missing the local folder (I'm used to navigating my hidden folders, so I did check it out properly), which is why I commented on it. Looking now, it's there.
It might have to do with this being a completely fresh install of my system. Either that, or I've been hallucinating.
This time, when I tried, I got this error:
neptunus-pc:~ neptunushirt$ cd /Applications/Mupen64Plus
neptunus-pc:Mupen64Plus neptunushirt$ ./rice.sh example.v64
dyld: Library not loaded: /usr/local/lib/libSDL-1.2.0.dylib
Referenced from: /Applications/Mupen64Plus/./Mupen64Plus.app/Contents/MacOS/mupen64plus
Reason: no suitable image found. Did find:
/usr/local/lib/libSDL-1.2.0.dylib: mach-o, but wrong architecture
/usr/local/lib/libSDL-1.2.0.dylib: mach-o, but wrong architecture
./rice.sh: line 1: 5623 Trace/BPT trap ./Mupen64Plus.app/Contents/MacOS/mupen64plus --corelib ./Mupen64Plus.app/Contents/MacOS/libmupen64plus.dylib --plugindir ./Mupen64Plus.app/Contents/MacOS --gfx mupen64plus-video-rice "$@"
Installing SDL had no effect. Scratchin' my head, right now.