Avalon Code. It has an in depth and almost pointless but highly addicting customization system. It's an action RPG for the record. It lets you adjust enemies stats and attributes and all sorts of stuff.
If you're not feeling in a battle-y type mood, there's Enchanted Folk and the School of Wizardy aka Magician's Quest Mysterious Times. It's like Animal Crossing but much more colorful and has a magic theme going on. I like it more than Animal Crossing as it has more to do and manages to keep the basic customization fun of Animal Crossing.
Ragnarok DS lets you refine weapons and armo to make them stronger as well as mount cards into equipment slots to cause different effects, and you choose how to distribute your skill points when you level up....