Let's see...
Fallout series
Final fantasy adventure/final fantasy mystic quest for original gameboy (not to be confused with mystic quest for SNES or any regular FF game). (note: tried to get into the remake 'sword of mana', but that manages to upgrade things in all the ways I dislike RPG's).
Secret of mana
Torchlight 2 (sorry diablo 3...torchlight 2 is just plain better)
Super paper Mario
Puzzle quest
Xenoblade Chronicles (though I have to admit I stopped playing at one point)
I'm probably missing a few (and I'm not sure titles like Okami, Muramasa: demon blade, Dust: an Elysian tail or sleeping dogs are eligible just because they've got a leveling system).