This list courtesy of Taron Millet’s Walkthru.
Dungeon Gold Skulltulas:
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 bomb able wall in the Deku tree. You’ll have to come back for it later. From start, it’s down the big hole, crawl through the small hole, then to your left behind a web.
Dodongo’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.
Dodongo’s Cavern – In the big stairway room, on the vines by the second floor doorway.
Dodongo’s Cavern – In the big stairway room, right above the big stairs in a small alcove. In order to get this one you have to return to the cavern after getting the boomerang and use the moving pillar in the big room to get to the second floor, then make your way back to this room and the stairs will be raised so you can get to it.
Dodongo’s Cavern – In the room before the boss’s room where you have to push some blocks around, there’s a bomb able door on the north end of the room. Bomb it open and kill the statue inside to reveal this one.
Dodongo’s Cavern – Go right from the main room into the hallway with the exploding lizards. To your left is an alcove. Use the scarecrow’s song and hookshot 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 skulltula in the same room.
Jabu-Jabu’s belly – On the vines in the room right before the boss.
Forest Temple – Entrance on vines on right wall.
Forest Temple – On the right wall of the big room, near the stairway opposite the entryway.
Forest Temple – In the East Plant Room on the wall on the Island. (use the hookshot on the chest to get on to the island.)
Forest Temple – In the West Plant Room on the wall , only reachable from the balcony.
Forest Temple – In the rotating room just before the boss, in one of the little alcove’s.
Bottom of the well – In the pit room (See Bottom of the Well walkthrough for details).
Bottom of the well – In the room next to the pit room (See Bottom of the Well walkthrough).
Bottom of the well – In the Shield-eater room (See Bottom of the Well walkthrough).
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 skulltula 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 skulltula 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 skulltula.
Fire Temple – Continue past the last gold skulltula and you’ll end up in the donut room where the megaton hammer is. To your left on the wall is a skulltula 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 skulltula 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 skulltula (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.
Shadow Temple – In the room with the ghost ship, stand on the platform next to the ship and play the Scarecrow’s Song to have Pierre appear across the way. Longshot over to get the skulltula.
Shadow Temple – In the room with the three rotating giant skulls, behind the skulls.
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 skulltulas 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.
Spirit Temple – As adult Link, in the room with the rolling boulders and the silver coins, in an alcove blocked by a blue Time block. Use song of Time. (Cool camera angle in there!)
Spirit Temple – As adult Link, in the room with the huge statue where you got the map, go up the stairs and play Scarecrow’s Song to hookshot across to a ledge with a gold skulltula.
Non-dungeon Gold Skulltulas (Most of these require it to be night to find them):
AL=Adult Link only, YL=Young Link only, neither=either link
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
Hyrule Field – As you leave Kakariko Village turn right and head to a small tree. Bomb the ground near it, drop down the hole. Skulltula is near ceiling
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
Hyrule Castle – AL – Go to the right of the castle and there’s a stone arch. It’s on the back of it.
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
Kakariko Village – YL – On a tree near the entrance
Kakariko Village – YL – On a red brick at the construction site in the middle of town.
Kakariko Village – YL – On the side of the house where the guard’s son lives.
Kakariko Village – YL – On that high tower in the northern part of town.
Kakariko Village – YL – The side of the rich cursed family’s house.
Kakariko Village – AL – On the wall above the chicken women’s house (use longshot to get up there)
Kakariko Graveyard – YL – On the southeastern wall.
Kakariko Graveyard – YL – Use bugs on the soft soil
Lost Woods – YL – The soft soil two screens left of the first area has one if bugs are used on it
Lost Woods – YL – The soft soil that’s R,L,R,L,L from entrance (use bugs)
Lost Woods – AL – The magic leaf platform R,L,R,L,L from the entrance leads up to one
Lost Woods – AL – To the east of the stairs in the Sacred Forest Meadow
Death Mountain Trail – In a cave behind a bomb able wall a little ways up the trail.
Death Mountain Trail – YL -In the soft soil at the entrance to Dodongo’s Cavern (use bugs)
Death Mountain Trail – AL – In a small nook above the entrance to Dodongo’s Cavern where the bomb plant was. Destroy the red rock there with the hammer to find it.
Death Mountain Trail – AL – After beating the Fire Temple, go up to where the rocks used to rain down on your head. Smash the red boulders there with the hammer and it’s behind one of them
Death Mountain– YL – In a crate just inside the crater (the mountain summit entrance)
Death Mountain – YL – Another soft soil spot near the crater. Use Bolero of Fire to get to it.
Goron City – YL – Smash open a crate on the top floor in a room full of boulders
Goron City – AL – On the side of the small stone platform suspended above the city.
Zora’s River – YL – In a tree at the mouth of the river
Zora’s River – YL – On the ladder near the entrance to Zora’s Domain
Zora’s River – AL – Just before the section with the waterfall is a bridge in a fairly narrow valley. Look very high on the left wall. You’ll need the Longshot.
Zora’s River – AL – Ride the magic leaf platform that’s at the beginning of the river (assuming you planted the bean as young Link there) and near the beginning of it’s trip it floats over a high platform with a boulder in the middle of a ring of rocks. Jump off onto this platform. Look high on the South wall and you should see it.
Zora’s Domain – AL – High up next to the frozen waterfall
Zora’s Fountain – YL – A tree on the small island in the Southeast corner (roll attack)
Zora’s Fountain – YL – Just to the right of the fallen log
Zora’s Fountain – AL – Pick up the gray boulder in front of the Faerie’s Fountain using the silver gauntlet to reveal a hole leading to one
Lake Hylia – YL – The small island with the two small pillars where you get the Fire arrows
Lake Hylia – YL – Behind the Lake Hylia Lab
Lake Hylia – YL – Use bugs on the soft soil next to the lab.
Lake Hylia – AL – In a crate at the bottom of the Lake Hylia Lab pool (use roll attack with Iron Boots).
Lake Hylia – AL – Above the Water Temple is a dead tree. Use your Longshot on a spot on the trunk just above the branch to get up and land on the branch. It’s on the top of the trunk.
Gerudo Valley – YL – When you first enter the valley and are walking across the plank look right
Gerudo Valley – YL – The soft soil spot on the ledge that you float to from the right side of the bridge using a chicken. Drop a bottle of bugs on it.
Gerudo Valley – AL – Look behind the tent on the back stone wall at night
Gerudo Valley – AL – On the left leg of the stone arch near the tent.
Gerudo Fortress – AL – There is one high above the eastern wall of the fortress
Gerudo Fortress – AL – In the horseback archery range on the Northern target
Haunted Wasteland – AL – Inside the stone structure where you discover the phantom guide.
Desert Colossus – AL – When you first get there, head left and it’s on a palm tree near a sand pit.
Desert Colossus – YL – A soft soil spot has one if you use a bottle of bugs on it
Desert Colossus – AL – The magic leaf platform from the previous one will take you to one.