There are three Bomb Bag upgrades (two in the European version), and here are their locations:
These are the locations and ways to get the bottles.
An easy way to kill a dark nut is to use the Dash Attack. If you use it, you will run right "through" him, and he will be confused for a while. Then, do it the other way to deal 2 hits on him!
You need all 8 Tiger Scrolls and the flippers. When you fuse kinstone with the swordsman trainer in Mt. Crenel it will open a waterfall passage in Castor Wilds. And when you fuse kinstones with the trainer in Lake Hylia it will open another waterfall passage in North Hyrule field. In both passages talk to the swordsman trainers there.
Here is how to unlock some extra goodies.
If you see a normal solitary tree, run into it and a fairy will come out.
To get the remote bombs, go back to Minish Village. Talk to the elder, then Kinfuse with him. Then, exit town via the northwest exit. Enter the house with the picori that gave you the bombs. He should give you the remote bombs. Lay a bomb down, then press that button again to detonate it whenever you'd like.
Note: Talking to the picori again while cause you to get the normal bombs again.
This shield upgrade can deflect more types of projectiles than the regular shield, and it's a lot larger. To get it, you must have beaten the game and saved, and completed the Goron sidequest (the one that gets you the bottle). Fuse with the Goron all the way on the right in the cave where you got the bottle; this will make Biggoron appear on top of Veil Falls, near the whirlwind which takes you to the Cloud Tops. Make sure you have a shield with you, and go talk to him. He will ask if he can eat your shield. Let him. Don't buy another shield, but come back a while later, talk to him, and he will give you the Mirror Shield.
In order to get the Magic Boomerang, first fuse with the Tingle Siblings, which reside in South Hyrule Field, Lake Hylia, Royal Valley and Lon Lon Ranch. They will each open up a tree in North Hyrule Field. There, you may find various things and a switch. Hit all four switches to open up the middle ladder. Inside is the Magic Boomerang.
There are a total of 3 quiver upgrades, and here are their locations:
Partway through the Temple of Droplets, you will come to ride a lily raft through some icy rooms. North of a room with flies (west and north of the refight with the first mid-boss) is a twisty room with a block puzzle. Use the raft to reach the first gate switch, but then abandon the raft and swim east, to a dead end. When you return, your raft should be gone, but if you cut across land to the end of the room, you should find it in the northeast, having already bypassed the puzzle. In addition, if you leave through the northeast door and come back, the block puzzle will be permanently solved.
To get the sound test , get 130+ figurines.Show the guy outside the cafe. He'll unlock Treasure Hut.(House with robot on top).
During certain points in the game, you will come across hidden Sword Dojos who will teach you a Special Sword Technique. But they will only teach you the Technique after you have a certain Item or have completed a certain task. Below, is the location of the Sword Dojo and the Requirement to learn the Technique
When you fuse kinstones with the postman running everywhere in Hyrule Town,
a girl will go into the post office next to the stamping guy. You can buy the swordsman newsletter for a huge price. Each issue contains tips to get around the secret areas of hyrule.
Go to the Inn and go where the three girls are. Go up to Farore and fuse kinstones with her. It should show the guy named "Gorman" going up to the locked house, saying he wants to rent it out. Go talk to him, and decide witch Goddess you want to give you a charm. Whatever one, go talk to her, and she goes to live in the house. Go talk to her in there, and she gives you a charm for your empty bottle.
There are three wallet upgrades, and here are their locations: