It is possible even without the hookshot or hover boots to get past the first gap in shadow temple and also the gap where you raise the bars after the truth spinner. This can be done as both child and adult link with a simple megaflip. Note that for the first gap, if you are doing a chu megaflip using pause buffering, you must be standing right at the edge for it to clear the gap.
In most speed runs, a player will either not have the lens of truth or magic, so the truth spinner must be done by guessing. A few things to note: There are 5 positions you can set the spinner, but it will always be one of the back 3, never the ones on the edges; thus, you have a 1 in 3 chance of getting it first try. It is also important that you do not fall in the pit if you are wrong, as this resets the room. You can either have ISG activated or have the Hover Boots on and start rolling away if the pit opens up. A few well-timed sidehops could get you away from the pit before it opens up too, but this is not recommended.
You can also do a distant megaflip through the gate, allowing you to not push the Truth spinner.
Right before entering the large main room, Navi will try to warn you about the Wallmasters. Simply store a ground jump and walk past to avoid it.
If you angle a superslide correctly from the main room, then equip the hover boots, you can hoverslide over to where the room with the Gold Skulltula, Like-Like, keese, and invisible scythe are. This saves time over going through the falling blades and around on a few invisible platforms.
In the room with the Gold Skulltula, Like-Like, keese, and invisible scythe, normally you must defeat all the enemies in the room to open the bars in the back for the Gold Skulltula. By manipulating the like-like against the gate, it is possible to perform a hookshot clip to get through. Once inside, you can simply walk out through the gate because only one side is solid.
In the room with two falling spikes, you are typically supposed to move the large block across the room to not get crushed. However, with a well-timed jumpslash, backflip, sidehop, or damage from the razor, it is possible to clip on top of the spikes. If you are in the air and under the spikes, you will not get crushed, but pushed through to the top, allowing for easy access to the switch and then the key.
Nearly the entire main section of the temple can be skipped using this trick. In the spinning scythe room there is a hole that leads down near the boat. Normally you would come from the other side and move the block and this would open up a shortcut straight to the boat. However, a well-angled jumpslash can clip through the gate near the boat, where the gate meets the wall. It is also possible to superslide through this gate-wall connection, but is rather difficult and uses explosives, so the jumpslash method is almost always preferred.
On the Virtual Console, the controller sensitivity is such that just flicking the control stick to the right will give you the correct angle.
In order to get up to the boat, you normally would push the block over, climb up it and then climb the ladder to the top. You could additionally just hookshot the top of the ladder. The fastest method, however, is a precise jump off the edge towards the wheel. If done correctly you can pop right on top of the boat's wheel, and then just sidehop to the middle of the boat. This is demonstrated at the end of the above video.
In the boss key room, there are two spike walls which slowly close in on Link that normally must be burned using Din's Fire or Fire Arrows. Instead, when you enter the room, immediately run over to the wall on the right and slash your sword at it, using the video as guidance for where on the wall to hit. This will activate the Redead behind the wall. Stay as close to the wall as possible (this will require taking damage) and soon the Redead should freeze you, allowing the walls to pass through you. When you're free, just kill the Redead and get the boss key. To escape, either wait until the walls come together (which causes the game to think you were crushed), or use Farore's Wind to warp out.
After riding the boat, there is a large gap you normally need to cross before you can head to the boss. This is supposed to be done by shooting arrows into the bomb flowers to blow up a statue, creating a bridge. There are three other methods that can be used:
Simply set up a superslide and then equip the hover boots to slide across the gap.
Do a chu megaflip or megasidehop from the broken piece of pillar, and equip hoverboots before you start to fall. A jumpslash can be added to ensure the landing on the other side.
It is possible, using a precise angle, to have a chu run across the gap and blow up the bomb flowers. See the video for details.
The Z-Target Ledge clip can be used with a damage boost to reach the loading zone.
The same can be done with a bombchu, but it is trickier to get the bombchu to explode in the right spot.
This uses 50 bombchus and is not used during a normal speedrun, but is worth documenting here for categories such as adult max %.
This has never been done on console and probably will never be done on console, due to the difficulty.
Although you are skipping the boat with the other methods, this one is considered as the best due to its speed. You need to use multiple glitches to pull it off.