Go to the tree that is near the bomb house. Angle yourself so that you are not perfectly parallel with the wall. A good angle indicator is the tree root that you are standing near. Slowly mover towards the stone wall and the ledge. Do a sidehop, immediately followed by a jumpslash to get around the stone wall. Now climb on top of the wall, and jump onto the roof.
Another version of this shortcut is to get higher using the roots of the tree and jumpslash over the wall.
It is possible to roll clip into the railing of the pirate ship and jump to the loading zone behind the door. First, make sure you have your sword out, and then climb up the ledge and target the wall as you do so. Hold directly left and do a roll clip, then target again and hold directly down. When link begins to fall, jumpslash to get back on the edge of the collision. Then C-up and put the B Button GUI somewhere near the ladder on the pirate ship. Then just do a sidehop and jumpslash and you should be in the loading zone.
Note: This setup only works on the original version of the game, since in the HD version, the loss of notches on the control stick make this particular setup nearly impossible. Another reason this trick is harder in Wind Waker HD is because you need to let go of the control stick immediately after roll clipping in order to prevent yourself from jumping to the ledge above.
You can skip the Password by getting door cancel off the door leading to jail. Once you have door cancel, maneuver your way onto the pirate ship and go through the door.
By using ledge clipping you are able to skip the entire password and enter the pirate ship directly after arriving at the island. Get one of the pots you can find on the island and walk with it to the ship. Place it on the left rail near the door and make sure it's as far out from the rail and so near the wall as possible without falling of. Use the Deku Leaf to grab the edge near the wall and push left at the frame Link's feet are straightened out. Drop the edge while you are out of bounds on the next frame and glide to the loading zone behind the door.
This is probably the easiest method of doing Password Skip; however, it is slower than the Roll Clip method. First, you need to set the wind to be southeast. Then, climb up onto the top ledge of the Pirate Ship. Now carefully maneuver yourself between the corner of the 2 crossing ledges. If done properly, Link will be partially inside the back wall of the pirate ship. Now let go of the ledge and pull out your leaf. Aim yourself so that you can land on the thin collision that's under the railing on the side of the pirate ship. Now walk carefully along the collision while inside the railing. Once you reach the edge near the side of the pirate ship that has the door, turn around, walk off the collision, and do a jumpslash to land on the very edge of the collision. Go into first person view and turn left a little bit. Do a sidehop and you should land in the loading zone.
If you got the Wind Waker Early, you can store Zunari's text to be able to move while buying the sail. This is a minor timesaver.
In 100% speedruns, you need to take a picture of Anton and Linda and a picture of Garrickson at the mailbox outside Windfall in order to obtain the deluxe pictobox. These characters take a very long time walking around the island however, so you will want to do as many sidequests as possible without reloading the area while waiting for the npcs to go to the correct locations.
The first thing you should do is start the hide and seek minigame, since starting that minigame resets Anton's position. Once hide and seek has started, try to catch all the kids except one and step onto the switch required to make the windmill turn. Then take both pictures. Make sure to not walk near Anton or Garrickson, as this will make them stop and make the waiting time longer.
If you have the Wind Waker early, you can do a few interesting strats. First off, it means you can learn the Song of Passing while waiting for the pictures. You can also setup a door teleport in order to reach your next destination faster once you have all the pictures. Finally, you can skip having to change the Wind direction to North to make the Windmill turn. To do that, get storage and press the switch. This will skip the short cutscene that shows that you did something to the windmill. Then leave the switch and press it again. Now, the next time you reload the area, the windmill will be turning, skipping the need for a northern wind.
Get storage and then shoot a fire arrow into the lighthouse. This will light up the lighthouse but you will still have control of Link due to storage. Then talk to Kreeb to get the heart piece. This skips all cutscenes associated with the lighthouse. Note that this permanently locks you out of the chest on the small island (chest that is required in NTSC/PAL 100% speedruns, but not in JP).
You can also shoot the torch through the walls on the side if you aim and time your fire arrow shot correcly, saving time since you can get the shot in sooner.
With chest storage, it is possible to climb the tree and get to Lenzo's house roof. it is then possible to clip OoB by going in between the 2 rooftops and roll into the loading zone. Normally, the door is unlocked by talking to Lenzo with the pictobox, and so this allows entering the house without it. This is not useful because in 100% speedruns it is required to enter that loading zone with the pictobox to get Lenzo and Minenco picture.
In Bug-Limit, it is important to be able to input the password to enter the pirate ship fast. While the suggested routes below are not optimal cursor movement, they avoid double-tasking control stick inputs and d-pad inputs.
1r4 = 1st row, 4th column
" = add the modifier (4th row, last column)
^ = add the modifier (5th row, last column)
↓↑→← = control stick
LR = D-Pad (cursor)
5r8 1r6 1r2 4r5 1r4"
Start ←↑←A ↓2←2A ←4A →2A X L ↓3→A Start
1r4 1r2 1r9 1r1 2r9
→3A ←2A ←A Start ←↓2A L2 ↑A Start
5r1 1r4 1r2 1r9 1r2" 1r13 5r6^ 2r9
↑2A ↓→↓A ←2A A X ←2A ↑←2↑←A X2 Start ←↓2A L4 ↑A Start
1r2 2r1 5r3" 3r2 1r2 2r2" 5r12 3r1
→A ←↓A ↓3→2A X ↑2←A ↑2A ↓A X ←↓A L Start ↑→A Start
1r4 1r2 1r9 1r5 2r3
→3A →A ←2↓A L2 ↑←A Start ←↓A Start
1r2 2r1 5r3" 3r2 2r5 3r2 1r7 3r3" Start
→A ←↓A ↓3→2A X ↑2←A A →A X L Start ←2↓A L2 ↓←2A Start