According to VGC database http://www.vgchartz.com/gamedb/?page=1&results=200&name=&platform=&minSales=0&publisher=&genre=Role-Playing&sort=JP the undisputed top are of course Pokémon, Dragon Quest, Final Fantasy, Yokai and Monster Hunter (if it is JRPG).
Then there are som old series like Chrono, Mana and SaGa that has sold more than a million per game, as have an old Eidos series: Dragon Warrior. Kingdom Hearts is also over one million, as is also Arc the Lad, Parasite Eve and Inazuma Eleven 2.
Below a million but more than half a million are games like: Xenogears, Seiken Densetsu, Tales of, Mario & Liugi, Earthbound, Star Ocean, Dragons Dogma, Paper Mario, Phantasy Star, Dark Souls and Fire Emblem.
All acording to our sponsor VGC database.
EDIT: Neither Ys, SMT or Persona have had a single game above 0.5 million in Japan according to the database. Is this really true?
