What aspects are you looking for? I can't remember exactly, but didn't they make Lufia where you can see the enemies on the map and fight them if you want to? And isn't Rune Factory like the Harvest Moon series (just with Fantasy stuff?). If you describe what sort of thing you are looking for, you may get more answers rather than just saying "like a game".
Well known farming sim is only Harvest Moon series & Rune Factory from Natsume. If you want to try other game with the same genre, Shepherds Crossing is your best bet. Available in NDS,PSP PS2 version. If you like fishing try River King Mystic Valley NDS,it's also from Natsume.My favourite so far is Atelier series from NIS I just love crafting system. You can get Atelier Annie for NDS. That's all I can think right now must say hybrid rpg like these are quite to find.