Death Mountain Peak
Near entrance of Goron Village there is a red flag. Follow the path near the flag up until you reach three boulders. Hop up past the first one and bomb the second one. Throw a bomb right before it explodes to blow up the third one. Continue up the path until you see the owl, go past him and bomb the wall for the fairy. You learn a neato spin attack.
Hyrule Castle
Climb the ivy and climb down the ladder past the gate of the castle. Go right until you see a sign that says "Dead End" and there is a rock there. Blow it up and fall down to the fairy. You learn Din's Fire here.
Zora's Domain
Go past the King and enter the room where Jabu-Jabu sleeps. Go to the left of Jabu-Jabu and swim until you see a little island with an errant rock on it. Guess what? Blow up the rock and fall down. You get Farore's Wind here.
Death Mountain
Inside the crater by the Fire Temple, there is a rock that must be smashed by the Hammer. Inside you get a double magic meter.
Desert
By the spirit temple you bomb the wall between two palm trees. Inside you get Naryu's Love, which protects you from enemy attacks temporarily. (Mini-note: Near the empty oasis, stand on a rock that you can Z Target and play the Song of Storms to make a fairy fountain.)