The Gold Skulltula side quest in Legend of Zelda: Ocarina of Time involves collecting 100 Gold Skulltula tokens from around all of Hyrule in order to release the curse on the inhabitants of the House of Skulltula. Check out the House of Skulltula side quest page to get an idea of the rewards that can be obtained for collecting tokens.
It can be fairly time consuming to go back and retrieve all of the Gold Skulltula tokens later on in the game. To make things easier, this guide points out all 100 Gold Skulltula tokens as they can be obtained during a regular playthrough. This page can be helpful though for identifying any that you might have missed.
Many of the Gold Skulltulas are revealed by releasing bugs on the mounds of soft soil located throughout Hyrule. Capture some bugs in a Bottle and then release them into the soil.
You can actually capture another bug as soon as you drop them as three separate bugs come out. One of the easiest places to obtain some bugs is near Hyrule Castle under one of the rocks.
Click on the locations below to be taken to that section of the guide.
1) Inside the Great Deku Tree:
In one of the first rooms of the dungeon – the same room that the Compass is located in.
2) Inside the Great Deku Tree:
Attached to the vines in the basement of the Great Deku Tree dungeon.
3) Inside the Great Deku Tree:
Attached to the bars in the basement of the Great Deku Tree dungeon.
4) Kokiri Forest:
Return to the Kokiri Forest at night time after Link is able to enter Hyrule Field.
5) Hyrule Castle:
Inside the Guard Tower on the way into Hyrule Castle Market.
6) Hyrule Castle:
Roll into the pine tree at the entrance to Hyrule Castle.
7) Lon Lon Ranch:
Roll into the pine tree to the left of the houses on the way into the horse pen area.
8) Lon Lon Ranch:
Enter Lon Lon Ranch at night and search the back of the horse pen.
9) Kokiri Forest:
Release some bugs on the mound of soft soil behind the Kokiri Shop.
10) Lost Woods:
Release some bugs on the mound of soft soil by taking a left and then another left in the Lost Woods.
11) Lost Woods:
Release some bugs on the mound of soft soil in the area where the Business Scrubs are located.
12) Kakariko Village:
Enter the village at nighttime and roll into the pine tree in the center of town.
13) Kakariko Village:
Enter the village at nighttime and search the house that is under construction.
14) Kakariko Village:
Enter the village at nighttime and search the back of the House of Skulltula.
15) Kakariko Village:
Enter the village at nighttime and search one of the houses near the entrance to the Death Mountain Trail.
16) Kakariko Village:
Enter the village at nighttime and search the large watchtower in the center of town to find one attached to the ladder.
17) Kakariko Village Graveyard:
Release some bugs on the mound of soft soil in the corner of the graveyard.
18) Death Mountain Trail:
Release some bugs on the mound of soft soil outside of the entrance to the Dodongo’s Cavern.
19) Dodongo’s Cavern:
Use the corpse of a Baby Dodongo to blow up a door.
20) Dodongo’s Cavern:
Attached to the vines in the room with the Bomb Flowers around the stairs.
21) Dodongo’s Cavern:
In a room with an Armos on the east side of the dungeon.
22) Death Mountain Crater:
Inside a crate near the entrance to the crater.
23) Death Mountain Trail:
Use a 
Bomb to blow up one of the walls along the trail.
24) Goron City:
Behind a wall of boulders and through a maze at the top of Goron City.
25) Zora’s River:
Roll into the pine tree at the entrance to Zora’s River.
26) Zora’s River:
Hanging on the ladder near the entrance to Zora’s Domain at nighttime.
27) Lake Hylia:
Release some bugs on the mound of soft soil beside the Lakeside Laboratory.
28) Lake Hylia:
Swim out to the island in the center of Lake Hylia to find one attached to the pillar at nighttime.
29) Zora’s Fountain:
Roll into the pine tree in the southeast corner of the lake.
30) Inside Lord Jabu-Jabu’s Belly:
Attached to one of the walls with vines early on in the dungeon.
31) Inside Lord Jabu-Jabu’s Belly:
In the room that Princess Ruto drops down into – requires the 
Boomerang to retrieve.
32) Inside Lord Jabu-Jabu’s Belly:
In the room that Princess Ruto drops down into – requires the Boomerang to retrieve.
33) Inside Lord Jabu-Jabu’s Belly:
Inside one of the later rooms of the dungeon attached to a vine wall.
34) Zora’s Fountain:
Located close to the large log in the center of the lake – requires the Boomerang to retrieve.
35) Inside the Great Deku Tree:
Returning to the basement of the dungeon. Use Bombs to gain entry to one of the back rooms and the Boomerang to retrieve the token.
36) Hyrule Field:Bomb a secret cave in the field and then use a Boomerang to obtain the token.
37) Kakariko Village Graveyard:
Attached to the back wall of the Graveyard – requires the Boomerang to retrieve.
38) Dodongo’s Cavern:
Return to the cavern, up to the second floor, through the east side, southwest and across the main chamber, returning to the room with the Bomb Flower and stairs that lower. Search the west side.
39) Lon Lon Ranch:
Attached to the upper level of one of the houses – requires the Boomerang to retrieve.
40) Lon Lon Ranch:
Attached to the forest near the silo – requires the Boomerang to retrieve.
41) Hyrule Field:
In a secret cave near the Gerudo Valley accessible with Bombs – requires the Boomerang to retrieve.
42) Gerudo Valley:
Attached to the waterfall near the entrance – requires the Boomerang to retrieve.
43) Gerudo Valley:
Use the Cucco to fly down to the lower platform down by the river and place some bugs in the mound of soft soil.
44) Lake Hylia:
Attached to the side of the Lakeside Laboratory.
45) Kakariko Village:
Enter the Village at nighttime and climb up to the roofs of the houses using the Hookshot. Located on the roof of the southern house.
46) Goron City:
Attached to the back of the wooden platform in the center of the city.
47) Ganon’s Castle:
Where Hyrule Castle used to be located – attached to the back of the archway.
48) Zora’s River:
South of the entrance to Zora’s Domain – requires standing on the fence to reach (with the Hookshot).
49) Zora’s River:
In the middle of Zora’s River attached to the forest on the south side.
50) Gerudo Valley:
Attached to the back pillar near the Master Carpenter.
51) Gerudo Valley:
Attached to the cliff behind the Master Carpenter’s tent.
52) Dodongo’s Cavern:
Enter the east side doorway into the room with the Baby Dodongos and play the Scarecrow’s Song to make Pierre the Scarecrow appear. Hookshot to the upper ledge.
53) Lost Woods:
Ride the Magic Bean Plant near the Business Scrubs area up to the upper ledge.
54) Sacred Forest Meadow:
On the eastern upper wall of the meadow.
55) Forest Temple:
In the first room of the temple attached to the vines.
56) Forest Temple:
In the large room of the temple near the back corner.
57) Forest Temple:
Atop the large island across the moat in one of the earlier rooms.
58) Forest Temple:
On the upper level far wall reachable by standing on the archway.
59) Forest Temple:
In one of the later rooms of the temple.
60) Kokiri Forest:
Attached to a house in the Kokiri Forest.
61) Hyrule Castle:
Inside a secret cave that can be accessed with the Song of Storms and using Bombs.
62) Bottom of the Well:
Inside one of the center rooms in the well.
63) Bottom of the Well:
Inside one of the other rooms in the center of the well.
64) Bottom of the Well:
One of the rooms at the back of the well.
65) Death Mountain Crater:
Release bugs into the mound of soft soil located in the Death Mountain Crater – requires the Bolero of Fire to warp to the crater.
66) Fire Temple:
Attached to one of the back walls in the middle of the temple.
67) Fire Temple:
Behind a wall that Link can use a Bomb on to reveal a hidden crevasse.
68) Fire Temple:
Part way through the Fire Temple attached to a chain-link fence.
69) Fire Temple:
In one of the top rooms of the Fire Temple.
70) Fire Temple:
In one of the last rooms of the temple behind a Like Like.
71) Death Mountain Trail:
Use the Megaton Hammer to destroy a red boulder near the Bomb Flower location.
72) Death Mountain Trail:
Travel further up the mountain to find another red boulder that can be destroyed.
73) Ice Cavern:
In one of the rooms part way through the Ice Cavern.
74) Ice Cavern:
Towards the end of the Ice Cavern.
75) Ice Cavern:
Attached to one of the back walls.
76) Zora’s Domain:
Use the Hookshot near the diving spot aimed at one of the cliff side walls.
77) Lake Hylia:
Enter the Lakeside Laboratory and use the Iron Boots. Roll into the crate and defeat the Gold Skulltula using the Hookshot.
78) Water Temple:
Attached to the walls behind the crystal switch.
79) Water Temple:
Part of the way through the Water Temple.
80) Water Temple:
In the room with the moving platforms with Hookshot targets.
81) Water Temple:
In the central pillar room reachable using the 
Longshot.
82) Water Temple:
In the room with the boulders attached to the back wall.
83) Lake Hylia:
Use the Longshot to reach the top of the tree on the center island at night.
84) Shadow Temple:
On one of the back walls of the temple.
85) Shadow Temple:
In the room with the spike walls inside one of the prison cells.
86) Shadow Temple:
Behind the large skull with blue flame.
87) Shadow Temple:
Use the Scarecrow’s Song to make Pierre the Scarecrow appear.
88) Shadow Temple:
In the room with three skulls with blue flame. The Gold Skulltula appears after all three are destroyed.
89) Gerudo Fortress:
On one of the eastern walls outside of the Thieves Hideout.
90) Gerudo Fortress:
On the target used for the Horseback Archery mini-game at nighttime.
91) Haunted Wasteland:
In the stone structure along the pathway to the Desert Colossus.
92) Desert Colossus:
Attached to one of the palm trees.
93) Desert Colossus:
Release bugs into the mound of soft soil outside of the Spirit Temple.
94) Desert Colossus:
Ride the Magic Bean Plant to reach one of the cliffs.
95) Spirit Temple:
Use the Boomerang to destroy and retrieve the token
96) Spirit Temple:
Attached to one of the climbable walls.
97) Spirit Temple:
Located above the doorway leading into the mini-boss room with the Iron Knuckle.
98) Spirit Temple:
Play the Song of Time to move a blue stone and open up the small crevasse.
99) Spirit Temple:
Play the Scarecrow’s Song to make Pierre the Scarecrow appear in the room with the large statue.
100) Zora’s Fountain:
Use the Silver Gauntlets to remove a grey stone and obtain the last token.
