There isnt necessarily a best version, they use different emulators. They are all provided so you can choose which you want to use.
You can see what is what by looking at /etc/emulationstation/es_systems.cfg
For SNES I use the retroarch pocketsnes version which is
/home/pi/RetroPie/roms/snes
For MAME I use mame4allpi, which is:
/home/pi/RetroPie/roms/mame
