IIRC the Wing Commander series supports Mice independantly of Joysticks, so you shouldn't need any conversion program... in fact most games will accept either.
Wing commander can not be played with a mouse, at least wing commander 1 through 3, can not. The default mouse control scheme makes it impossible to control.
Have you tried ppjoy?
I did a google search for "Joystick Emulator" and that seemed most promising since Mouse->Joystick is supported. No idea if it works well though.