.nes for cartridges, .fds for Famicom discs. Although the emulators can emulate both NES cartridges and Famicom disks just fine, Batocera has the systems split up into two separate entries, /userdata/roms/nes for NES and /userdata/roms/fds for Famicom. Put your ROMs in their respective folders, and then if you want you can group the systems inside of EmulationStation so that they share a menu.