For boss and miniboss strategies, see the pages for Aeralfos and Argorok.
You can use two LJAs to cross over the first room without using an Ooccoo. For the first LJA just wait until the boomerang is over the void, for the 2nd you can hit the pillar to make the boomerang come back faster and hence be quicker.
Opening the door to the hub of the dungeon from far enough way will prevent Link from hitting the trigger that activates the fan blocking the way to the boss key. This can be done by opening the door carefully as wolf. This saves around 1:30 for Any% and All Dungeons, 5 seconds in 100%, and some time in No S+Q as well.
You cannot hit the trigger for the fan while transforming, so it is safer to transform right before the door so the animation will bump your backwards and in the correct position. This is slightly slower than approaching the door as wolf, but is much less risky.
This method involves transforming to wolf before reaching the door, which can save time on movement but makes it harder to avoid hitting the fan trigger.
At either spinner socket in City in the Sky, there is time just before the bridge finishes extending to drop off of the spinner and roll twice. However, getting two rolls requires getting off the spinner as soon as possible, which is risky because the bridge will fully retract if Link stops spinning too soon. It is much more lenient to only aim to get one roll in. To do so, drop off the spinner once the end of the bridge reaches the range bounded by the red lines in the image below. The cue is the same for both bridges, just mirrored.

LJAing over the gap after the first spinner socket is faster than clawshotting, even with a two-handed grab and extra equips. The video below shows three approaches. For all options, it is important to stand near the edge of the platform, but be aware that it's easy to fall off of this ledge.
When you open the first small key within City in the Sky, a cutscene trigger is added at the end of the bridge that you came in from, and your savewarp point is changed to start you off next to the small key chest until the cutscene is triggered. This savewarp spot is incredibly convenient because you return to this room immediately after obtaining the Double Clawshots, which saves some backtracking.
After obtaining the first small key, head back outside and cross the bridge. Target the last peahat and sidehop onto the banister on the right on GCN (it will be the last broken chunk before the staircase). Jump to the next banister then head back into the dungeon through the broken grate window, staying clear of the door at the end of the bridge.
Alternately if you don't feel you will make the sidehop before the wind starting blowing you can clawshot onto the last peahat, look towards the window then drop and jump attack to get past the trigger. This is slower however.
This displacement clip modifies the standard rollstab setup slightly because the coordinates' high values in City in the Sky cause rounding errors. See notes on displacement clip setups.
However, note that if Link is on critical health (1 heart or less), the standard rollstab setup can be used instead after lining up with the gate. In this case, after the clip, LJA across and then drop down without skipping any floors to avoid taking fall damage.
There are multiple ways to get down to Aeralfos's door after the clip. The gate can also be skipped with a displacement clip rupee dive, but that method is harder and slower.
Press B to jumpslash when the area in the red box hits the top of the screen.

In step 3, lining Link up with one of these green boxes gives him a working z-position for the clip.

In step 3, aligning Link's heel with the line on the ground shown below while targeting and in the leftward-moving stance gives him a working z-position for the clip. This area has significant lag on console when the camera is facing the gate, but using this cue keeps the camera facing away from the gate for almost the entire trick.

Optimally, this is slightly slower than using a visual cue to align Link, but it doesn't involve eyeballing his position. After getting the cardinal facing angle, sidehop into the left side of the door frame, then slash turn 180 degrees.
Shown below is a comparison between two methods of getting to the door with an LJA, as well as outcomes from clanking or bad wind RNG.
This displacement clip uses the standard rollstab setup after sidewalking into the right side of the door frame. If at critical health (1 heart or less), this same setup works in the middle of the door. See notes on displacement clip setups. This saves around 5 seconds (with the improved setup below) over pulling the switch.
After entering the Aeralfos room, there is one frame for input between the door locking animation and the camera turning. Since the iron boots are required to pull the switch, it's optimal to use this frame to put on the iron boots, aim and shoot the clawshot at the switch as soon as you regain full control, and then hold down to make Link descend on the clawshot while the switch is being pulled. This is how other options compare:
This grate clip skips the outside section of the traditional early boss key sequence by doing a skewed Clawshot shot through the part of the grate that's missing hit detection, onto a small grate above. Shown below is a quick setupless method. The first visual cue is at the tip of the triangle shown in the video. After Link begins to fly towards the target, hold down and the Clawshot button so that Link descends a consistent amount. Aim to the left until aiming at around the edge of the bottom grate. If done correctly, the reticle should snap to the side, allowing you to Clawshot all the way up to the small grate.
Troubleshooting:
Shown below is the easiest and fastest way to back up a failed clip. Once you know the clip won't work, simply Clawshot the bottom grate where you're aiming. Hold down and the Clawshot button like before to sink a set amount, turn Link around, then simply Clawshot at the correct position on the bottom grate (the same spot you aimed for during the initial Clawshot). Proceed with the rest of the trick as normal.
Setup by gymnast86: here
Setup by Glubbers: here
Setup by Draconif: here
Instead of clipping through the grate outright, Wii can use the reticle displacement in third person aiming to find the upper grate above. Note that for this to work, Link has to be dangling from the grate with his right hand and clawshotting with his left.
It is possible to skip turning the northern fans on on the way to the fan tower. Clawshot onto the first two fans high up in their clawshottable areas and from above so that Link grabs the tops of the fans. From there, use LJAs to reach the exit door as shown in the videos below.
Use quick double clawshot aiming to be able to make the cycles.
The last two shots of this path make it somewhat harder than the standard path, but it is 3s faster. Note that the positioning on the first fan is not as precise as the video makes it look, but because the crystal switch hit must be delayed for the fans to line up properly, there's no reason not to take time to get into the corner.
The two methods below are the only known ways to achieve this skip on GCN. Wii can use a 3rd person clawshot clip instead.
This displacement clip saves 14s over not skipping the room. It does not use the standard displacement clip setup as the goal is just to clip into the wall and then clawshot through. See notes on displacement clip setups.
Be careful: Pressing L in most places at the bottom of this room will lock onto the cylinder, which is not useful for the setup.
This setup is about 2s slower than the setup with hidden skills. Be careful: Pressing L in most places at the bottom of this room will lock onto the cylinder, which is not useful for the setup.
This method is extremely precise and is not recommended.
An LJA to skip the three clawshottable pillars is possible but very precise.
Roll 4 times to stand on the very edge of the blocks, then aim in line with the wall and throw the boomerang as high as possible. LJA as soon as the sword is out. Roll 3 more times and clawshot the peahat to make the cycle without waiting. Roll towards the north edge and target the wall, then LJA onto the broken wall of the island with the poe, B-Charge the poe from the wall and collect it. If done correctly, you should have enough time to clawshot back. It is then possible to LJA across the gap to the heart piece chest.
If you don't clawshot up to the island peahat early enough to lock onto the next peahat and make it back, rather than wait out the cycle, it is faster to get onto the rim of the island and clawshot back to the vine wall. The three best methods of doing this are shown in the video below:
If you clawshot onto the very edge of the vine wall, Link will be in clawshotting mode rather than climbing mode. If this happens, clawshot up to the peahat and then back down to the vine wall or to the peahat behind the vine wall.
It is possible to skip transforming wolf and going on any ropes in the area before the boss key room. To do this stand next to the door and clawshot the vines, you should barely reach. From here you can stand on the edge and target on the ceiling above the door and LJA across, this works because the boomerang is over the door frame which is higher ground
Using a bomb arrow to hit the top fan tower switch from the floor can save around 8 seconds over ascending the tower normally. Using two bomb arrows can save even more time but is extremely difficult.
To set up the bomb arrow shot on the upper crystal:
This video compares the options and shows the double BA strategy, though it uses a slower path for the single BA than in the video above.
On Wii, you can't target walk off of a ledge with Clawshot out, which is advantageous here.
Skip clawshotting vines (slower)
Roll through the first two fans. Then to get past the last fan, equip the iron boots, and quickly sidehop across the falling blocks.
AKA Double Dyno Skip :]
Using a 3pcc, it's possible to skip the block room, the room with the two dynalfos (hence "double dyno skip"), and the oocoo jump room, and saves over a minute in glitched categories that complete this dungeon.
Steps in more detail below:
Roll through the first two fans, then go towards the diagonal ledge. Make sure the sword is out. Then, either target walk forwards, or roll towards the ledge and then let go of the stick to ledge grab. You want Link to grab the ledge as far right as possible without the wind blowing you. Do not adjust further to the side after grabbing the ledge, as this may put you behind an invisible wall. Once Link is grabbing the ledge, let go, and jump attack once he is below the wall. Too early and he will either clank, or not clank but still get pushed back by the wall. Too late and he won't make the jump.
The gate clip is easy and consistent with pointer controls disabled. With pointer controls turned off, run into the corner, and then pull out clawshot and start aiming to the left. Once the reticle is aligned with the thin white line, aim up a little bit (not precise) and release clawshot to clip through. The video below explains visual cues. Note that it takes about 8.5 seconds to enter the options menu twice to disable and later re-enable pointer controls.
The gate clip is slightly more finicky with pointer controls enabled, but still consistent. Enter the door coming from B2 of fan room as close to the center as possible so that Link is facing due west. Once entered, sidehop and target roll. Enter first person and aim to the left until the right pole is flush with the edge of the screen. Pull clawshot on the left half of the screen, and then aim just to the right of Link's earring. This may take a few tries based on your exact angle and exactly how you moved the pointer after pulling clawshot. The video below explains visual cues.
You may want to utilize turnarounds to normalize Link's facing angle before the sidehop.
There are various ways to get to the door, with the fastest being instantly throwing the boomerang to perform a keese LJA, which requires good RNG with where the keese is. The video below demonstrates various methods to get to the door quickly.
Since boomerang Long Jumps can't be done on the Wii version, instead throw the boomerang at the keese conveniently located near the gap. As the boomerang starts to return towards you, target the keese in order to do an LJA. Repeat this process to cross the final gaps.
After clawshotting to the second falling pillar, aim back at the first falling pillar. Shoot the clawshot once the bottom of the pillar (indicated in blue below) passes the right corner at the bottom of the central column (indicated in red below). Link will only be pulled to the falling pillar until it starts freefalling, which lands him right by the door if timed correctly. This saves 1s over clawshotting to the top of the room as intended.

Quickly get from the door to the rough area shown at the very end of the video below. Press the clawshot button while tapping target, releasing target, and then re-pressing target and holding it. If done correctly, this should lock onto the nearby baba serpent and then the peahat, and releasing the clawshot will make it reach the peahat before it gets too far away. This requires getting to the right area somewhat quickly, but the trick doesn't require perfect movement, as the examples in the video below demonstrate. Having the clawshots in Link's hands already can make reaching the peahat faster but is not required.
If failed, the best backup can either be to attempt the wolf method (next section) or to void out and try again. After a void, the trick is easier because the peahat takes longer to get out of reach than it does when coming from the door.
This jump is somewhat precise but does not require a dash. Because the peahats continue moving during Midna calls and transformations, this is not any slower than other methods when using the peahat LJA to cross the next area.
It's possible to LJA to the HP chest without using the boomerang. Simply stand near the edge of the block, target the Peahat, and when its in position jump attack to make it across.
This saves about 17s traversing the peahat cycle room in the context of completing the second half of City in the Sky in reverse. It is exclusive to Wii NTSC 1.0 because that is the only version on which the bars in this room are clawshottable.
After entering the room or voiding out from the poe island, clawshot to the peahat on the left. Drop immediately and time a jumpslash to land in the hole. The jumpslash timing is more lenient the closer the peahat is to the wall. Jump down, then clawshot up to the bars. Stand roughly where shown and clawshot clip by aiming the clawshot far to the right.
If you fail to jumpslash from the peahat to the hole in the wall, voiding to try again costs about the same amount of time as clawshotting up the vines and taking the slow peahat cycle that the clawshot clip skips, so retrying is not recommended.
With precise clawshots, it's possible to get across without using LJAs of any kind. This can be around 5-10 seconds faster than turning the fans on (more in categories like 100%, which already have the boss key upon room entry), give or take, depending on aim and ledge grab + kargarok RNG. Having to sometimes deal with the kargaroks makes this a little bit riskier, but it's still manageable. The video below demonstrates the fastest method, along with backups.
The videos below demonstrate the fastest way to clawshot up the fan tower, with and without bomb arrows.
It is possible to CAD the cylinders in the compass room by falling off the chest, then interrupt the CADs with bombs to position the cylinders in precise locations. It is then possible to perform Jump Strike Moon Boots to reach one cylinder, LJA to the next, and finally clawshot to the upper floor, skipping the small key on the west side of the dungeon.
Instead of going the intended route past the fans, you can go to the right and LJA over to the door. Try to make the boomerang bounce off of the doorframe so you don't need to wait as long to LJA.
There are many ways to get through the block room before the double dynalfos. The fastest method for GCN is to roll around the right side, LJA using the tileworm, and then boomerang LJA to the exit. This method and several others for GCN are covered in the tutorial video below.
Roll near the ledge. Once the dynalfos jump, shoot the clawshot to scare them into the void. The timing for shooting the clawshot is somewhat precise.
For an easier alternative that is only slightly slower, run straight for the center of the platform on the other side of the room, and perform a spin attack. This will knock the two Dynalfos off of the platform. Quickly target the vines with the clawshot, and grapple to them before the cutscene begins.
It is possible to skip turning on various fans in this room with a well angled jump with an Ooccoo. Use the 2nd fan to get atop the broken wall with Ooccoo, angle yourself towards the ledge, hold target, and then hold forward to jump. Then, drop Ooccoo at the correct time to grab the ledge. If you fall straight down instead of jumping, it means you were angled too far right and walking into the wall; if you do fly but are too low to grab the ledge, it means you jumped off too low or took an unnecessarily long flight path.
This is slightly faster than picking up the Ooccoo but costs 2 hearts.
Please note there is a faster way to complete CitS by getting the Boss Key Early.
This saves 5 seconds. Stand on the very edge as shown in the video, aim just to the left of the structure and throw the boomerang, if you LJA as soon as possible you will land as shown and be able to clawshot up skipping a clawshot target.