Hyrule and Lorule are brimming with hidden Rupees and secret passages. Always be on the lookout for suspicious cracks in walls, especially in dungeons and caves; these often indicate bombable sections leading to hidden rooms, chests, or shortcuts. Similarly, look for discolored patches of ground or unusual rock formations, which might hide secret entrances when bombed or hammered.
Many areas also contain invisible paths or platforms that are only revealed by using the Lamp or by observing subtle environmental cues. Don't hesitate to use your items in unexpected ways; for example, the Tornado Rod can sometimes reveal hidden switches or clear away debris. In Lorule, pay extra attention to areas that mirror Hyrule's geography, as a secret in one world might have an equivalent in the other. Thoroughly exploring every corner of the map, including underwater sections with the Zora's Flippers, will often yield valuable Rupee stashes or even Pieces of Heart.