Jupiter, the company that made The World Ends With You, also developed a series of downloadable Picross games for the Nintendo 3DS. There’s a special one with a Nintendo theme, but you can’t buy Club Nintendo Picross from the eShop. You have to exchange Club Nintendo points to get this game.
Club Nintendo Picross has puzzles with Animal Crossing, Mario, and The Legend of Zelda in it. Altogether, there are 86 picross puzzles and 2 micross puzzles. The game costs 80 Club Nintendo points in Japan.