there is a 64bit version of Mupen64Plus for linux but not for windows
if i remember rite there is some difference be-twine 64bit linux and 64bit win
which makes the 64-bit Dynamic Recompiler incompatible with 64bit windows
The 32-bit version will run fine on 64-bit windows. The reason that we have a 64-bit version for Linux is that some linux distros do not have all the necessary 32-bit compatibility libraries, and therefore need a native 64-bit version. Since the 32-bit version actually runs faster though, it's better to run this one if you can. On Windows, there's no problem running the 32-bit build under the 64-bit OS.