Keits:
Err, that's N-Rage, a windows plugin.
OP specified that he's using Mupen under Linux.
reuabreliz:
Which plugin are you using? The Mupen control plugin does not allow for keys to be altered, they're hardcoded in.
Blight's SDL plugin however should work fine, or should at least detect the keyboard. Please be sure to have selected the correct mode of input using the button on the top right.
The plugin works well for many people, however is not solid.
If you're still having trouble, try mupen64plus, there are many improvements in stability and features over the old vanilla mupen64 v0.5 that I assume you're using by posting in this forum (and not the mupen64plus forum).