Note: All D-pad controls for the Wii Remote are for the perspective the Wii Remote is when held in the currently-selected menu navigation mode.
Do you want the best possible controls on WiiMednafen? If so, following this guide will hopefully help you as I tell you the optimal controls for menu navigation and system emulation for WiiMednafen.
Menu (I'm not sure if you can change this)
Nintendo Entertainment System default controller, Game Boy or Game Boy Color (yes, you can use the same controls when emulating the Nintendo Entertainment System default controller, Game Boy or Game Boy Color in WiiMednafen)