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: