It depends on the system and the emulator. The file format most commonly used for NES ROMs does not include region information, so most NES emulators require the user to manually select NTSC or PAL timing to match their ROMs. I think SNES emulators should automatically use the correct framerate though, as the SNES ROM header does include a region field.

The NES/SNES minis always use the NTSC versions of the game, regardless of region.