Here are where all the Gold Skulltulas are, remember you can only get them at night.

- LEGEND -

YL - You can only get it as Young Link
AL - You can only get it as Adult Link
EL - You can get it  as either Link
BL - You can only get it using both Links

- The Rewards for Killing the Skulltulas -

10 Skulltulas - Adult's Wallet.  Allows you to carry 200 Rupees.  
20 Skulltulas - Stone of Agony.  Makes your Rumble Pak (if you have one) rumble 
when there is a nearby secret.  
30 Skulltulas - Giant's Wallet.  Allows you to carry 500 Rupees. 
40 Skulltulas - Bombchu.  An unpredictable bomb that can travel up walls.   
50 Skulltulas - Heart Container peice.  
100 Skulltulas - Big rupee worth 200 Rupees, can get it infinite time. Lame!!

Kokiri Forest: 

1 - YL - In the back of the Know-It-All Bros. House.
2 - YL - Drop a bug on the plot of soil next to the Item Store.  Out pops 
a Skulltula!
3  - AL - In the back of the House of Twins.

Hyrule Field: 

4 - EL - Plant a bomb inside of the stone circle in front of the Gerudo 
Valley entrance to uncover a cave.
5 - EL - Plant a bomb next to a tree on the east side of Hyrule Field.

Hyrule Market: 

6 - YL - Bash into a box in the Guard Room (the room with all the 
pots).

Hyrule Castle:

7 - YL - Bash into the tree straight ahead from the entrance area.
8 - YL - Play the Song of Storms near the tree where you first 
met Talon.

Lon Lon Ranch: 

9 - YL - Bash into the tree near the entrance.
10 - YL - On the back of the small corral shed.
11 - YL - On the outer wall, northwest of the storage shed (the room 
with the two cows).
12- YL - On second story window of Talon and Malon's house.

Kakariko Village: 

13 - YL - Bash into the tree near the entrance.
14 - YL - On the side of the House of Skulltula.
15 - YL - On the stack of bricks.
16 - YL - On the side of the Graveyard Kid's house.
17 - YL - On the observation tower (on the ladder).
18 - AL - On top of Impa's House.

Kakariko Graveyard:

19- YL - On the outer wall, right of the Royal Family's Tomb.
20 - YL - Empty a Bug onto the plot of soil.

Lost Woods: 

21 - YL - Go left from the start, and then go through the log at the end of 
the area.  Empty a Bug onto the plot of soil.
22- YL - Go to the area with the tall grass and the Forest Stage.  Empty a 
bug onto the plot of soil there.
23 - BL - Plant a Magic Bean in the soil for Skulltula 2 as Young 
Link, and come back as Adult Link, where you will find a Magic Plant that will 
take you up to a platform where a Skulltula is hiding.

Sacred Forest Meadow: 

24 - AL - Climb up on top of the hedges in the hedge maze, and, 
assuming you're facing Kokiri Forest, it's on the left outer wall.

Death Mountain Trail: 4 Gold Skulltulas

25 - YL - Drop a Bug onto the plot of soil in front of Dodongo's Cavern.
26 - YL - Inside the first bombable wall on the right side.  Once you 
kill it, you CAN get the Token - it doesn't look like it, but the wall IS 
climable.
27 - AL - Smash the red boulder in the area where you threw the 
Bomb Flower to open up Dodongo's Cavern.
28 - AL - Smash the red boulder in the volcanic eruption area.

Goron CIty: 

29 - YL - Go to the Boulder Maze room (on the top floor), and make your 
way to the end.  Bash the crate there.
30 - AL - Go to the center platform suspended by ropes, stand on one 
of the side ropes, and fire your Hookshot at the Skulltula on the back of the 
Goron's Ruby holster.

Death Mountain Crater: 

31 - YL - Bash the crate at the entrance to the area.
32 - YL - Drop a bug onto the plot of soil.

Zora's River:

33 - YL - Bash the tree at the entrance.
34 - YL - On the ladder near the waterfall in front of Zora's Domain.
35 - AL - Near the Fairy Fountain at the top area.  From that 
platform, check the south outer wall, and bag the Skulltula.
36 - AL - Look up and to your left while on the bridge near the 
waterfall, and you'll see it.  Jump up on the fence past the bridge, and the 
Hookshot will just barely reach.

Zora's Domain: 

37 - AL - Go to the area where the Zora man gave you the Silver Scale 
(above the waterfall).  Stand on the edge of the platform, look to your left, 
and you'll find it.

Zora's Fountain: 

38 - YL - Bash the southeast corner tree.
39 - YL - On the outer wall, west of the fallen log.
40 - AL - Lift the boulder near the Fairy Fountain entrance 
where you got Farore's Wind.  You'll have to go through an area infested with 
invisible Big Skulltulas before you reach the Gold Skulltula.

Lake Hylia: 

41 - YL - On the back of the Lake Hylia Laboratory.
42 - YL - Empty a Bug onto the plot of soil in front of the Laboratory.
43 - YL - On the Fire Arrow platform.
44 - AL - Grapple to the top of the tree (where the Serenade of Water 
Warp Point is).  It's harder than it sounds.
45 - AL - Sink to the bottom of the pool in the Laboratory, and bash 
the crate there.  I didn't know spiders could survive in water..

Gerudo Valley: 

46 - YL - Empty a Bug onto the plot of soil at the bottom of the canyon.
47 - YL - On the waterfall opening (the mini waterfall near the 
entrace, not the huge one).
48 - AL - Behind the carpenters' tent.
49 - AL - Under the stone arch across from the tent.

Gerudo Fortress: 

50 - AL - Go to where you can grapple to the treasure chest containing 
the Piece of Heart, and look down in the big gap, along the outer wall.
51 - AL - On one of the horseback archery targets.

Haunted Wasteland: 

52 - AL - Inside the stone structure where you meet the invisible 
ghost.

Desert Colossus - 

53 - YL - Warp to the Spirit Temple using the Requiem of Spirit, and empty 
a Bug onto the plot of soil near the entrance.
54 - AL - On the palm tree by the dry Fairy Fountain (pond).
55 - AL - Use the same Magic Plant you used to get the Piece of 
Heart to get to the high stone platform on the right.

Inside the Deku Tree -
56 - YL - 1F, in the room with the three rising platforms, on the south 
side.
57 - YL - B1, on the vines leading back up to 1F.
58 - YL - B1, on the wooden bars at the north side of the room.  The 
Token can be acquired by jumping.
59 - YL - B1, in the room behind the bombable wall.

Dodongo's Cavern - 

60 - YL - 1F, behind one of the bombable walls that the Baby Dodongos 
destroy.
61 - YL - 2F, on the vines in the room where you blew the stairs down.
62 - YL - 1F, the northern-most room, behind the Armos.
63 - YL - 2F, in the stair room, there's a Skulltula in a hidden 
alcove if you look up and forward from the stairs.
64 - AL - 1F, in the room with the Baby Dodongos, 
summon Pierre using the Scarecrow Song when Navi turns green, but there doesn't 
seem to be anything there.

Inside Jabu-Jabu's Belly: 

65 - YL - B1, on the vines inside the room with the switch and 
rising water.
66 - YL - B1, after you drop down the hole where the green tentacle 
used to be.
67 - YL - B1, same area as Skulltula 2, if you look closely.
68 - YL - 1F, on the vines, in the final room before the Boss.

Forest Temple: 

69 - AL - 1F, on the vines in the very first room.
70 - AL - 1F, in the main room (the one with the four torches), to the 
right of the northern-most door.
71 - AL - 1F, in the northeast part of the northeast courtyard, on the 
wall.
72 - AL - 2F, in northwest courtyard, against the wall.
73 - AL - B2, in the rotating wall room (the final room before the 
Boss).  It's hidden behind a wall.

Fire Temple: 

74 - AL - 1F, play the Song of Time to move a Time 
Block so that you can get to a secret door.
75 - AL - In the rolling rock maze, bomb a wall that sounds hollow with 
your sword.  To give you a hint, the view will change dramatically (to a view 
right behind Link) when you're in the right area.
76 - AL - When you get to the area above the rolling 
rock maze, look up and to your left, where Navi will turn green.  Summon Pierre 
using the Scarecrow's Song, and grapple to him.  
77 - AL - Keep going past Skulltula 3, and you'll 
come to an area with a huge pit.  There's a Skulltula on the wall above the pit.
78 - AL - In the second spinning tile room, right before the 
area with the Boss Key.

Ice Cavern: 

79 - AL - Against the wall in the room with the huge spinning ice 
blades.
80 - AL - In the room with the Piece of Heart, right next to it, 
against the wall.
81 - AL - In the ice block sliding puzzle room, against the wall (left 
from the entrance, I think).

Water Temple: 

82 - AL - In the center room in the main area, very high against the 
wall.
83 - AL - In the room with the waterfall hookshot platforms (it's on 
the right wall from the entrance).
84 - AL - In the room with the switch behind a closed gate.  Use a Spin 
Slash to hit it.  It's behind the closed gate.
85 - AL - In the whirlpool river room, midpoint, against the wall.  
Use the Iron Boots to keep yourself from moving.
86 - AL - In the room where the boulders drop down from the waterfall, 
right before the Boss Key.  It's behind the waterfall, against the wall.

Bottom of the Well: 

87 - YL - In the room behind the left-hand locked door in the center 
room.
88 - YL - In the room behind the right-hand locked door in the center 
room.
89 - YL - In the upper-right area, in the same room as the Like-Like.  
Watch out!

Shadow Temple: 

90 - AL - In the room with the invisible spinning scythes.
91 - AL - In the room with the falling spiked celings, behind a cell.
92 - AL - In a room with a Skullpot.  You can find it behind the 
Skullpot.
93 - AL - In the room with the floating ghost ship.  
You can either attempt to hit it while the boat is moving (very hard), or you 
can summon Pierre using the Scarecrow Song to get up close and personal.
94 - AL - Behind the three spinning Skullpots.

Spirit Temple: 

95 - YL - In one of the silver-rupee collecting rooms.  It's on the 
fence.
96 - YL - Behind the ladder, at the top, in the room with two 
Lizalfos.
97- YL - Above the doorway in the hall right before you fight Iron 
Knuckle.
98 - AL - In the silver-rupee collecting room with the rolling 
boulders.  Play the Song of Time in front of the Time Block to reveal the 
Skulltula.
99 - AL - In the room with the huge snake 
woman/goddess/thing statue.  It's on the inaccessible platform at the left side 
of the room, against the wall.  You can either use the Longshot to nail it, or 
you can summon Pierre using the Song of Scarecrows to grapple to it.

Ganon's Castle:

100 - AL - Go to the general area where the guard gate used to be 
(where you had to sneak past in order to get into the castle grounds).  There, 
you'll find the last Gold Skulltula on the side of the stone structure.

You should now have all 100 gold skulltulas, yeah!!!!!