Bottom of the well - In the room next to the pit room .
Bottom of the well - In the Shield-eater room .
Fire Temple - In the big lava room with the bridge (first room you go through) on the far North side there's a blue block above the doorway.  Play the song of time to move it and go through the new door that's revealed.  The gold Skultulla is in that room.
Fire Temple - In the maze like room with the large boulders everywhere, one of the walls can be
blown open to reveal a gold Skultulla in a small alcove.  Walk along the outside walls and listen for it.  It's in the northeastern part of the room.
Fire Temple - In the room with the Shield-eater just before the boss key room.
Fire Temple - On the second floor of the boulder maze above the doorway there is a high platform. Use the Scarecrows song and hookshot to it.  Then hookshot over to a platform across from it and it will lift you to a secret area that has a gold Skultulla.
Fire Temple - Continue past the last gold Skultulla and you'll end up in the donut room where the
megaton hammer is.  To your left on the wall is a Skultulla you can get with the hookshot.
Ice Cavern - In the room with the helicopter blade thing made out of ice.
Ice Cavern - In the small round room East of the helicopter blade room.
Ice Cavern - In the room with the moving block of ice, West of the helicopter blade room.
Water Temple - Above the second vortex in the underground river.
Water Temple - Inside the tower in the middle of the main room, at the top.  Need longshot first.
Water Temple - Behind the waterfall in the room with the boulder rolling right before the boss key.
Water Temple - High on the right hand wall in the room with the big waterfall and the platforms
going down it.  Need longshot.
Water Temple - There's a passageway on the bottom level (left from the passage that leads to where you meet Ruto) that leads to a dead end with a gold Skultulla behind a grate.  Use a power spin move (hold A and charge, then release) next to the grate to hit the shock switch inside and open the grate.
Shadow Temple - In a room on a side path from the giant room with the falling blades.  Go left
instead of right after fighting the Stalfos, go through the door, and kill the enemies to open a door
leading to the Skultulla (This one's in the walkthrough).
Shadow Temple - In the room with the falling spikes in a cage to the left.
Shadow Temple - In the room with the single giant skull there's one behind the skull.