To use the Shard of Agony you must have a Rumble Pack inserted into your controller. When you get near one of these hidden holes, the Rumble Pack will start to vibrate. Now you must do one of three things. To uncover the stone you must either play the Song of Storms, place a bomb nearby, or smash the ground with the Megaton Hammer. One of these methods will open the hole and leave its treasures for your taking.
Location: On your way to Gerudo Valley from Hyrule Castle there is a single tree standing by itself.
Reward: Inside of this hole there is a piece of heart at the bottom of a pool of water.
Location: Near the Hyrule Castle moat there will be a tree nearby.
Reward: There are three walls that can be broken down by a bomb. Behind one of the walls is a Golden Skultula.
Location: Ouside of the Sacred Forest Meadow entrance.
Reward: After defeating two Wolfos you will get a purple rupee.
Location: In the middle of a small ring of stones near Gerudo Valley
Reward: By using Din’s Fire you uncover a cow, a gossip stone, and a Golden Skutula.
Location: Between the fences that blocks the path to Lake Hylia.
Reward: Inside this hole is a Buisness Scrub that will sell you a piece of heart for 10 rupees.
Location: Middle of Kakariko Village Courtyard.
Reward: Defeat the 2 Redead to get a Huge rupee.
Location: Across the bridge on the way to Kakariko Village
Reward: A Golden Skutula.
Location: On ledge near Gerudo River.
Reward: The hole is filled with rupees. You must dive for them though.
Location: Ring of Stones outside entrance to Goron City.
Reward: Gold Rupee inside of chest.
Location: Under a boulder in the Lost Woods.
Reward: A Buisness Scrub will sell you a Deku Nut upgrade for 40 rupees.