The Gold Skulltulas are probably one of the more enjoyable parts of the game. Finding all of them yeilds certain prizes, and certain advantages. The list below tells the location of every single Skulltula you can find in the overworld of Ocarina of Time.

KEY *= only as a kid
**= only as an adult
(if its blank that means it doesn't matter what age you are)

Kokiri Forest
* There is a Gold Skulltula behind the Know-It-All Brothers house, this can be found at night only.
* Drop some bugs in the bean hole to sprout a Skulltula
** There is a Skulltula behind the Twin's House. This can only be found at night.

Lost Woods
* The bean hole in the area past the Skullkid sprouts a Skulltula, just toss in some bugs.
* The bean hole with the two Buisness Shrubs and the entrance to the Forest Stage has a bean hole. Drop in some bugs and claim your prize.
** After planting a bean in the hole by the two Buisness Shrubs, return as an adult and ride it up and claim your Skulltula, but beware! this is a night only deal.

Hyrule Field
In the tree to the left of the Castle entrance is a Skulltula
There is a Skulltula in a hole by the Gerudo Valley entrance.

Hyrule Castle
* Inside the Guard House at the entrance to the Market is a crate with a Skulltula inside.
* Play the Song of Storms at the gate to Hyrule Castle
* At the tree near where you found Talon sleeping, play the Song of Storms, a hole will open up and a Skulltula is inside.
** Behind the stone arch is a Skulltula

Kakariko Village
* Outside the entrance to Kakariko Village run into the tree and a Skulltula falls out
* There is a Skulltula behind the House of Skulltula, this is at night only
* Behind the house near the gate to Death Mountain trail is a Skulltula, this is at night only
* On the ladder of the watch tower is a Skulltula, at night only
** At night kill the Skulltula on the wall behind and above Impa's house

Graveyard
* Shove a bug in the hole and watch your Skulltula pop out!
* Check the wall on the right side of the Graveyard at night. There is a Skulltula there.

Zora's River
* The ladder, at night, by the waterfall has a Skulltula
* In the tree before where you meet the Owl is a Skulltula
** Against the right valley wall, by the entrance at night, is a Skulltula
** At night there is a Skulltula along the left wall as you walk past the bridge to the Waterfall

Zora's Domain
** At the top of the frozen waterfall is a Skulltula

Zora's Fountain
* In the tree by the Great Fairy Fountain is a Skulltula
* On the wall by the big fallen log is a Skulltula, at night
** At night go to the Great Fairy Fountain, use the Silver Gauntlets to lift the rock and bomb the stone underneath. Use the Lens of Truth to dodge the invisible Big Skulltulas and climb the ladder and kill the Gold Skulltula in the crevice

Lake Hylia
* At night, swim to the island where you got the Fire Arrows. On it is a Skulltula
* At night there is a Skulltula behind the Labratory
* Drop some bugs in the hole by the Labratory and claim your prize
** The big tree on has a Skulltula on it, at night
** There is a Skulltula in the crate at the bottom of the Lab's pool

Goron City
** Use the Hookshot to get the Skulltula behind the inscription stone on the raised middle platform
* In a crate in the big rock room on the top floor is a Skulltula

Death Mountain
In the cave at the beginning of Death Mountain is a Skulltula
* The entrance to Dogondo's Cavern, in the bean hole, has a Skulltula, I think you know what to do...
** Past the large Valley with the falling rocks is a Skulltula on the right wall, at night
** At the area where you tossed the bomb flower at the Dogondo's cavern is a Skulltula behind the red rock, at night though

Death Mountain Crater
* There is a Skulltula in the bean hole, you have to be quick about getting it though! You'll need to play the Bolero of Fire to get there
* In a box at the entrance to the crater, the summit one, is a Skulltula

Gerudo Valley
* At night there is a Skulltula on the wall by the wood plank
* The bean hole in the large crevice has a Skulltula
** At night there is a Skulltula behind the tent
** Under the stone arch, at night, is a Skulltula

Gerudo Fortress
** At night there is a Skulltula on the wall behind the Fortress
** At night there is a Skulltula on the one of the targets at the Horse Back Archery place

Haunted Wasteland
** Inside the stone house where the Poe Guide is is a Skulltula

Desert Colossus
** At night, in one of the palm trees at the dried up oasis is a tree
** At night, ride the bean platform to the plateau and kill the Skulltula on it
* Do the whole bug thing with the bean hole

Lon Lon Ranch
* Outside of Talon's window, at night, is a Skulltula
* At night, check behind the shed in the Corral for a Skulltula
* There is a Skulltula in the tree in the Corral

Sacred Forest Meadow
** At night there is a Skulltula on the east side of the stairs

NOTE: There are more Skulltulas outside of Dungeons, this is just a list of the ones I have found. Come back often for updates!