It is possible to skip the Skull Kid Cutscene you first encounter when you're about to enter the path to Swamp, by playing the Song of Double Time right when you enter the cutscene. Simply line up to the spot shown in the video and perform a sidehop. Then pull out the ocarina before link touches the ground. If you press the ocarina button too early, it won't work.
By doing a sidehop (or a backflip) onto the seam like shown in the video, you can go to Mountain Village early without the Bow.
You can also lure a Chuchu up next to the blocked path and do a recoil flip off it to clip past the ice.
You can do a precise Long Jump to get onto the fence as Human Link to skip having to get Epona to jump over the fence. The Jump Attack to the fence is frame perfect, so it is recommended to Home Buffer it.
By simply luring a Chuchu next to the fence and doing a Goron Pound and canceling it in midair you can get hurt by the Chuchu and land on top of the fence skipping having to get Epona and explosives.
By using the Chu Jelly next to the deku flower at the southern entrance to Clocktown you can get a Flower Slide to get past the barricade to the path that leads to Great Bay. Using the map on the touchscreen as a guide is recommended.
When you void out in the water as goron multiple times, the game will respawn you back to where you last came in from instead of next to the where you drop. After a day transition your coordinates update to where you were last standing. Doing this void out glitch in a grotto will respawn goron link according to the coordinates of the last area, and this can be used to respawn you outside the grotto either out of bounds or in other unloaded grottos.
"Grotto AE" for short. By doing Extended Hookshot in the grotto with the dodongos, you can clip into an unused grotto (only used in the Japanese version of Majora's Mask) to exit out in Deku Palace. Since the entrance was never removed, this is possible.