Make these achievements to get the indicated result:
Silver Keys: complete each level with at least 1000 rupees, then defeat Vaati.
Gold Keys: complete each level with at least 3000 rupees, then defeat Vaati.
Hero Keys: complete each level with at least 5000 rupees, then defeat Vaati.
Super bomb: complete the Ice Palace followed by the Misery Mire Maze, then go to your house in the Dark World and buy the orange and white bomb.