Neogeo CD is supported! But everyone uses the arcade one because it's much better.
EDIT: to answer your question...
snes is rather hit or miss, you really need to try it out for yourself. I doubt mario rpg will run well because, if I recall correctly, it uses special hardware.
there really is only one neogeo cd emulator, only one neogeo emulator, and only one MAME emulator, you shouldn't have trouble figuring that out
stick with regular Neo-Geo for now, Neo-GeoCD emulation isn't anywhere near as good yet. The roms will be much smaller than the CD images anyway, so you have more room for, say, MAME or Genesis
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