I am running Ubuntu Dapper Drake and mupen64 v0.5. Downloaded, unzipped/tarred, and I get this:
ben@btw-ubuntu:~/mupen$ ./mupen64
Couldn't read config file '/home/ben/.Trash/mupen/.//mupen64.conf': No such file or directory
Bus error
ben@btw-ubuntu:~/mupen$
From my googling it looks like this...