Snes:
the Fire Emblem series (not so unknown now, thanks to the translation patches available)
Bahamut Lagoon
Inindo: Way of the Ninja
Albert Odyssey (I think there's a translation patch available for this now)
Sailor Moon: Another Story (laugh all you like, it's miles ahead of the average licensed game)
Live a Live
the two Lufia games
Romancing Saga 1-3 (be warned, these games turn you loose with very little handholding. It's easy to end up with no idea what your next step should be)
Rudra no Hihou (again, I'm not certain if theres a translation available for this game)
Genesis:
Langrisser 2
the Phantasy Star series
the Shining Force series
Uncharted Waters 2
Ys III
I don't have access to my PSX or N64 roms at the moment, so I can't really name any from there.