The default is FCEUmm
http://wiki.libretro.com/index.php?title=FCEUmm
You can change this when you start up a game, press x or m, this will bring you to a menu screen that lets you change the emulator.
The other choice there is nestopia
http://wiki.libretro.com/index.php?title=Nestopia
https://github.com/libretro/nestopia
