According to Wikipedia: http://en.wikipedia.org/wiki/Sandbox_games So games like Viva Piñata & Zoo Tycoon 2 DS fit the bill.
scribblenauts IS a sandbox game. Post Merge: [time]1285396730[/time] a sandbox game is something which you can run around and can do whatever you want. What you do in scribblenauts depends on the user.
If they base themselves on Book 2, the new Golden Sun will probably be a sandboxie-like RPG. Anyway, I hate this kind of game, so there is no way I can suggest anything like that D:
It's sandbox because of the actual way you complete those challenges, which isn't fixed. The game tries to encourage you to think up different scenarios using your imagination. I hate Scribblenauts though. A good idea implemented way too poorly. That's personally one of the things i liked about GS2. You could go about doing sub quests, to upgrade your weapons, collect different summons etc. I hate RPG's that force you to complete the story and nothing else.