Death Mountain Crater:

• Near the entrance from Death Mountain Trail, there is a box. Roll into it to reveal a Gold Skulltula.

Death Mountain Trail:

• There is a small mound of soil right by the entrance to Dodongo's Cavern. Drop some bugs on the soil and a Gold Skulltula will pop out.
• At the beginning of Death Mountain Trail, near the entrance to Kakariko Village, the is a bombable stone wall. Blow it away to find a Gold Skulltula. The token will be kind of high up, but you can climb the wall to get it!

Dodongo's Cavern:

• In the room first room off the right platform from the main room, there are Baby Dodongos in a zigzagged corridor. On the right side, there is a bombable wall. If you've got mad skills, you can try to kill one of the Baby Dodongos near the wall so it will blow the wall when it explodes. But that junk is hard. Come back when you can carry bombs and blow the wall away. Go through the door and kill the three Keese. The Gold Skulltula is on the far wall.
• In the room with the large stone steps and the domino bomb flowers, go up the steps by the door. There is a Gold Skulltula on the vines opposite of the door.
• In the same room, look past the vines across the room. There is a hole in the wall with a Gold Skulltula in it. I'm not sure how you're supposed to get it. I'm not sure the boomerand could reach it at that angle. Maybe come back as an adult and get it with the longshot?
• After you bomb the Dodongo statue's eyes, enter his mouth. Take the passage to the right. In that room is a bombable wall. Beyond the bombable wall is a room with a Gold Skulltula. Be careful, there's an Armos in front of the Gold Skulltula.

Goron City:

• On the top level, all the way on the left side, behind the stones in the way, there is a room with a LOT of stone. Some are tan, some are reddish brown, some are gray. If you only have bombs at your disposal, blast away the tan stones and follow the maze they make. At the end is a little clearing with box. Roll into the box to reveal a Gold Skulltula.

Graveyard:

• Enter the Graveyard at night. In the far right corner, there is a Gold Skulltula on the wall. However, he is pretty high up. Link will not be able to reach the token without the boomerang.
• When you enter the Graveyard, go up the hill to the left. There is a mound of soil by the wall. Drop a bug on the soil and a Gold Skulltula will pop out.

Great Deku Tree:

• Enter the Great Deku Tree, climb the ladder up to the spiral platform. Climb the vines to the circular platform and enter the door. Step on the switch in the room and jump to the platform in front of you, then to the platform to the left, and on to the ledge. There is a Gold Skulltula on the wall.
• Break the spiderwebs on the floor in the center of the main room. Fall into the hole. There will be a Gold Skulltula on the vines you use to climb out of the hole.
• Break the spiderwebs on the floor in the center of the main room and fall into the hole. In the water, there will be a barred tunnel. On the bars is a Gold Skulltula.
• Break the spiderwebs on the floor in the center of the main room and fall into the hole. Find the room with the Gohma eggs on the ceiling. In this room is a different wall which can be bombed away. Behind the wall is a Gold Skulltula.

Hyrule Market:
As a child:

• After you cross the draw bridge but before you get into the main part of the market, go to the room with all the pots. There is a Gold Skulltula in one of the boxes.

Hyrule Castle:
As a child:

• Roll into the tree before the gate and a Gold Skulltula will fall out.

Kakariko Village:

• At night, roll into the tree near the entrance from Hyrule Field and a Gold Skulltula will fall out.
• At night, there is a Gold Skulltula on the outside wall of the House of Skulltula.
• At night, there is a Gold Skulltula on the ladder of the tall observation tower.
• At night, there is a Gold Skulltula on the outside wall of the little boy's house, near the gate to Death Mountain Trail.

Kokiri Forest:

• Enter the Kokiri Forest at night. There is a Gold Skulltula on the back of the House of the Know-it-All Brothers (to the right of the entrance from Hyrule Field).
• Drop a bug in the mound of soil outside the Kokiri Shop and a Gold Skulltula will pop out.

Lon Lon Ranch:

• Enter the main corral area of the Ranch and roll into the tree to the left. A Gold Skulltula will fall out of the tree.

Lord Jabu-Jabu's Belly:

• Enter Lord Jabu Jabu, go through the first room, then go through the door the left. Follow Princess Ruto down the hole, then go throw the door behind you. Go through the hallway into the room with a ditch of water. Shoot the Gold Skulltula to the right. Bing careful of baddies, step on the switch in the ditch to make the water rise. Swim to the right and climb up the vines (or whatever those things are) to get the Gold Skulltula token.
• After defeating the green parasitic tail, exit the area with the Tailpasarans into the room with the holes. Fall into the hole to your right where the green electric current used to be. From the platform you land on, you can get a Gold Skulltula on the wall using your boomerang.
• After defeating the Bigocto, get on the platform that bring you in to the ceiling. Go through the area until you ride a platform down into the room before where you first met Princess Ruto. Grab one of the two boxes and use the newly lowered platform to get to the switch. Leave the box on the switch and enter through the door. On some of the vines in this room is a Gold Skulltula.

Lost Woods:

• When you first enter from Kokiri Forest, take the tunnel to the right. Go through the next tunnel, pass the Skull Kid, and there's a mound of soil on the ledge. Drop a bug on the soil and a Gold Skulltula will pop out.
• When you first enter from Kokiri Forest, take the following tunnels: right, left, left, right, right. You should be in an area with two Business Scrubs. There's a mound of soil by the Business Scrubs to the right. Drop a bug on the soil and a Gold Skulltula will pop out.