Here's a complete list: Don't use it if you want to have fun
Deku Tree
1.) On the second level walkway, behind a crate near the Gohma eggs.
2.) In the 2F room where you found the compass. Play the Song of Time in the spot where Navi turns green, then climb on it and bomb the boulders up top.
3.) Graveyard room. Play the Song of Time to make a time block appear. Climb on top the get the hidden Skulltula..
4.) In the small room to the northwest, adjacent to the graveyard room. You have to have the hookshot or boomerang to get it.
Dodongo's Cavern
5.) In the room next to the giant stairway mechanism. Walk towards the back of the room and play the Song of Time. This will make some of the blocks disappear. Jump in the holes and play the song again to clear the adjacent block. The Skulltula you seek is in the southeast corner.
6.) In the room where you fought the Lizalfos, northeast, behind a row of boulders (need bombs to blow up)
7.) On the first floor, in the room with the two Deku scrubs. Use the hookshot or boomerang.
8.) In the northern room before the Boss (with the bouncing statues). Stand on the top glass step and jump towards the wall to the left.
9.) Underneath a crate in the small room northeast of the main hall on the second floor
Inside Jabu-Jabu's Belly
10.) Underneath a time block in the oval room with the Boomerang on B1
11.) In B1, west, room (with invisible enemies). Requires fire arrows and Lens of Truth.
12.) In the room right before the boss, behind a spider web (use boomerang).
13.) In northwest room on the first floor (second branch from the left where the path splits).
Forest Temple
14.) First hallway, 2F in the upper right corner of the hallway above the door..
15.) Rectangular room, 1F/2F (west). Turn left first and go around the corner to find a Skulltula on the ground.
16.) Outdoor area, northeast, 1F. Above the doorway, sitting on a hookshot target. Take it out with the hookshot and collect the emblem.
17.) In the sewer (after draining the water), on the grate.
18.) When climbing out of the sewer, at the top of the vine.
Fire Temple
19.) Lava lake, 1F: on the wall behind the Goron.
20.) Second floor, play the Scarecrow song where Navi turns green.
21.) Diagonal room, north, 3F. Defeat the Lizalfos, then take out the spider on the wall to get another emblem.
22.) Round center, left tower, 3F: The wall in the niche to the right is fake. Blow it up and get the Skulltula emblem. Go back into the main tower.
23.) Small round chamber, 4F: Use your hookshot to destroy the Skulltula and pull in the emblem.
Ice Cavern
24.) Square room, northwest, where you fought the Ice Wolfos. Play the Scarecrow's Song to get up to the spider.
25.) In the same room, in the south. Play the Song of Time and melt the red ice..
26.) In the north cave with the blue flame. Make the time blocks appear and melt the red ice.
Water Temple
27.) Tunnels, southeast, 2F: Stand in front of the closed gate in the middle of the area and use Din's Fire. This will kill the spider and open the gate. Grab the emblem, then exit and turn right.
28.) Underground river, 2F: Look up when you're on the third target.
29.) Dodongo room, B1: in the area behind the iron grate.
30.) From the main hall, enter the south tunnel on the bottom floor. Go through the tunnel until you reach a long room in the south portion of the map. Stand on top of the hookshot target. Climb up the steps and play Scarecrow's Song. Hookshot your way up to the scarecrow, then light the torches at the far end of the room with your Fire Arrows (make sure you have enough magic power to fire at least three arrows) to open the gate and get the spider. The Skulltula is on the ceiling of the small room..
31.) Storage room, west of the main hall, 2F: Use the hookshot to get into the small room just above this one on the third floor.
Bottom of the Well
32.) In the small room filled with invisible enemies in the center of the dungeon
33.) Mummy's tomb, east, B1: Find the spider behind a pillar in the back of the room.
34.) Dank cave, B3: in the northwestern arm of this cave.
Shadow Temple
35.) Trap room, south, B4: push the block underneath the two mashers and enter the cell.
36.) Redead meeting room, B4: on wall.
37.) Mummy chamber, B4: on top of a pile of who-knows-what.
38.) Boat dock, B4: Play Scarecrow's Song and use hookshot.
39.). After the boat arrives, cross the bridge and jump off to the left, then turn around and look back. On the wall below the "river of the dead" fog layer..
Spirit Temple
40.) Large room, west, 3F: in the southeast corner on top of a block.
41.) Sand filled room, east, 1F
42.) Spider's lair, northeast, 1F. On the left wall next to the door.
43.) Battle room, 4F, hidden behind the left set of thrones. Have the knight strike them.
44.) Same room, behind the thrones straight at the end of the room.
As for the rest of the Skulltulas, you're going to have to venture all over Hyrule as both an adult and a child. Most of the Skulltulas can be found at night, but there are some that you can find during the day. Others can be found in certain and sometimes confusing situations.
* Tip: Bug trick: If you buy or catch a single bug in a jar, you will end up with three when you empty your jar. Recatch one of the bugs from your jar and there will be three bugs from it when you empty the bottle again.
AS YOUNG LINK
Kokiri Forest
45.) Back of Know-It-All-Brothers' house.
46.) Put a bug in the soft soil near the Kokiri shop.
Hyrule Castle
47.) In a crate in the guard tower at the castle gate.
48.) Roll into the first tree across from the vines.
49.) Go past the guards through the castle moat. Play the song of storms near the tree and bomb the walls inside the hole.
Kakariko Village
50.) In a tree near the entrance.
51.) On one of the brick walls at the incomplete house.
52.) On the side of the house across from the guard gate.
53.) On the watch tower ladder.
54.) On the side of the cursed Skulltula house.
Graveyard
55.) On the wall to the right opposite side of the entrance.
56.) Plant bugs in the soft soil.
Lon Lon Ranch
57.) On the side of Talon's house.
58.) On wooden wall to the left of the cow shed.
59.) On the back of wooden part of the corral, north of the entrance.
60.) In a tree near the corral where cuccos hang out during the day.
Lost Woods
61.) From the entrance of the Lost Woods, take two lefts. Cross under the bridge to the pile of soft soil and plant a bug in it.
62.) From the entrance, go right, left, right, left, then left and find the soft soil.
Death Mountain
63.) Bomb secret cave on right side of trail.
64.) Plant a bug in the soft soil in front of the entrance to Dodongo's Cavern.
65.) Climb death mountain and enter the death mountain crater. Break open the box on the inside.
66.) Break the crate on the top floor (in the same room with the different colored rocks).
67.) Plant a bug in the soft soil inside the death mountain crater (use bolero of fire to reach soil.)
Zora's River
68.) On the ladder near the entrance to Zora's Domain.
69.) In the first tree you see when you enter the river.
Zora's Fountain
70.) In the tree on the small island.
71.) To the right of the fallen log.
Lake Hylia
72.) On the small island with the two pillars (same place where you get the fire arrows).
73.) On the side of the Lake Laboratory.
74.) Plant bugs in the soft soild next to the lab.
Gerudo Valley
75.) Look to the right of the plank over the small waterfall.
76.) Look to the right side of the gate on the bridge and you'll see a ledge. Jump to the ledge using the chicken and plant a bug in the soil.
Desert Colossus
77.) Find the soft soil next to the entrance of the Spirit Temple and plant a bug in it.
AS ADULT LINK
Hyrule Field
78.) Smash the red boulder near the entrance of Gerudo Valley. Bomb a hole in the ground and use Din's Fire near the cow and find it around that area.
79.) In hole to the left of the Hyrule Castle bridge.
Kokiri Forest
80.) Back of the Twins' House.
Ganon's Castle
81.) On the back of the arch that used to be the guard gate.
Kakariko Village
82.) On the wall on the roof of the house next to the chicken pen (longshot needed).
Lost Woods
83.) Opposite end from the entrance of the sacred forest meadow on the right side wall.
84.) Go right, left, right, left, and left then ride the magic bean platform (plant bean as child first).
Death Mountain
85.) Go to where the bomb plant was used to open Dodongo's Cavern and break the nearby rock open with your hammer.
86.) Smash one of the red boulders where the volcano used to erupt as you walked through.
87.) On the side of the small platform in the middle of Goron City.
Zora's River
88.) Look up high on the left wall after the bridge (longshot needed).
89.) Climb up the ladder on the small ledge on the way down the river. At the top of the ladder you'll see a circle of rocks and one big rock in the middle. Turn to the left of these rocks and find the Skulltula hanging on the wall.
Zora's Domain
90.) Stand on the edge of the frozen waterfall and shoot the skulltula on the left side.
Zora's Fountain
91.) Pick up the boulder in front of fairy fountain (silver gauntlet needed).
Lake Hylia
92.) At the bottom of the Lake Hylia lab in a crate (iron boots needed).
93.) Shoot the trunk above the tree branch of the dead tree to land on the branch itself. Kill the Skulltula on the trunk by standing at the edge of the branch and hitting it with your hookshot (tree is located by warp point to the water temple).
Gerudo Valley
94.) Behind the Carpenters' tent.
95.) On backside of stone pillar across from carpenters' tent.
Gerudo Fortress
96.) On dirt wall above center entrance to fort.
97.) On target pole at archery range.
98.) On back of palm tree near fairy fountain.
99.) Inside stone where you found phantom guide.
100.) Ride magic bean platform (plant bean as child first).
Show Posts
But thats never going to happen..maybe the dino part will, but the future car thing...I don't think so. 
