Some walls, trees and stones now carry short notes that Navi can read for you. These Fairy Thoughts point to secrets – several of the new Pieces of Heart below only make sense once you have read the right note.
Many of these secrets need both eras. They are easiest to finish once you can switch freely between child and adult, which is the case after the Forest Temple.
Pieces of Heart that need both eras
The locked chest near Gerudo Valley: a small chest sits under a rock overhang in Hyrule Field, close to the path to Gerudo Valley. As a child you cannot open it, and as an adult you find it already emptied. Read the Fairy Thought next to it in the adult era, then visit the chest again as a child – now it opens and holds a Piece of Heart.
The scrub who wants a password: bomb the cracked ground beside the moat, just east of the Castle Town drawbridge. The Business Scrub in the grotto below only deals with customers who know the password. Come back as an adult, read the Fairy Thought on a tree close to the grotto to learn it, then return as a child, give the password and buy the Piece of Heart for 100 Rupees.
The Skulltula grotto in the wetland: as a child, bomb the cracked ground in the small marshy area of Hyrule Field where several Peahats float around. A Fairy Thought in the grotto asks you to get rid of the Skullwalltula there. Defeat it, then return to the same grotto as an adult – a Gold Skulltula has taken its place.
Other spots that are easy to miss
Business Scrub in Death Mountain Crater: as a child, hurry down from the crater entrance towards the broken bridge. A Business Scrub on a low ledge there sells a Piece of Heart for 100 Rupees. The Piece of Heart that used to be in the Ice Cavern is no longer there – this one takes its place.
The man on the roof in Kakariko: carry a Cucco up the hill behind the windmill and glide from there onto the blue roof of the potion shop. The man relaxing on the roof is so pleased to have a visitor that he gives you a Piece of Heart.
Inside the windmill: after you win the Hookshot in Dampé's race, the way out leads into the windmill. Use the turning platform to reach the high ledge with a Piece of Heart.
Treasure Chest Shop: with the Lenses of Truth you can see which chest holds the key in every room, so the Piece of Heart at the end is a sure thing.
A hidden grotto at Hyrule Castle: as a child who knows the Song of Storms, sneak past the guards to the spot near the castle where you first met Malon. A plant with propeller-shaped leaves grows by the tree there – play the Song of Storms next to it to open a grotto, then bomb the cracked walls inside for a Gold Skulltula.
A tunnel at Lake Hylia: swim from the island with the big tree to the southwestern shore. A narrow ledge there leads into a tunnel you can squeeze through; a Gold Skulltula waits at its far end.
Side activities
A cow for Link's house: once you ride Epona as an adult, take on Malon's obstacle course at Lon Lon Ranch. Beat her record time and a cow moves into Link's house in Kokiri Forest. Bring an empty bottle and play Epona's Song next to it for free Lon Lon Milk.
The running man: as a child you will see him jogging laps around Hyrule Field. If you carry the Bunny Hood from the mask trade, he buys it and pays as many Rupees as your wallet can hold.
Racing the running man: in the adult era he rests in the tent in Gerudo Valley and challenges you to a race to the bridge at the Lost Woods. He always finishes ahead of you, so treat it as a time trial rather than a race you can win.