YOUNG LINK ONLY:

Deku tree - In an alcove on the left side of a room on the third floor.
Deku tree - Room you fall to when falling through web.  On vines.
Deku tree - Room you fall to when falling through web.  On grate.
Deku tree - Behind the only bombable wall in the Deku tree. From start, it's down the big hole, crawl through the small hole, then to your left behind a web.
Dodonogo's Cavern - In the passageway to the right of the entrance into the big room, in a secret room on the right wall of the passage.  Blow up the doorway by killing an exploding lizard next to it.
Jabu-Jabu's belly - On the vines in the room with a switch in the middle that raises the water level.
Jabu-Jabu's belly - In the room you fall to after falling through a pit.
Jabu-Jabu's belly - Right next to the previous gold Skultulla in the same room.
Jabu-Jabu's belly - On the vines in the room right before the boss.
Spirit Temple - After crawling through the hole at the beginning as young Link, go through the right door and it's on the fence across the pit.
Spirit Temple - After crawling through the second small hole as young Link, climb up the rock face where the regular Skultullas are and then turn around to see the gold one.
Spirit Temple - As young Link, after the room where you have to move the blocks to get the sun symbol into the sunlight you'll be in a staircase.  It's above the door you entered through.
Hyrule Field - AL - Find a circle of stones near the entrance to Gerudo Valley, smash the red boulder with the hammer, bomb a hole in the ground, then use Din's Fire to find it behind a web and a cow
Kokiri Forest - YL - Back of Know-It-All-Brother's house
Kokiri Forest - YL - Drop a bottle of bugs on the soft soil by the shop and one will pop out.
Kokiri Forest - AL - Back of the Twin's House.
Hyrule Castle - YL - In a crate inside the guard house at the market entrance (roll attack to open)
Hyrule Castle - YL - The first tree you see when entering the castle grounds (roll attack it)
Hyrule Castle - YL - After getting past the outside guards in Hyrule Castle's grounds, swim down the moat to the corner where there's a big tree.  Play Song of Storms, drop down the hole, and bomb the walls
Lon Lon Ranch - YL - Near the roof of Talon's house on his second story window
Lon Lon Ranch - YL - In a tree near the entrance to the ranch, roll attack to get it
Lon Lon Ranch - YL - Behind the shed at the edge of the corral
Lon Lon Ranch - YL - Outer wall of the ranch, just north of the stone structure