It depends upon the console. Sega Consoles as well as the tg-16, c64 and msx have limited configuration options by editing a text file in the ccf archives, nes, snes, n64 and neogeo, however, do not. The reason you can't remap a nes or snes game is pretty obvious as the wiimote/classic controller are specifically designed for these systems. Every single neogeo title has the same layout and n64 titles have a custom emulator for each individual game and thus it made no sense for the emualtor authors to offer any form of configuration.