There are 3 bomb bags to obtain and 1 capacity upgrade that affects all 3 bags.
Go to the fishing hole, and find the sign that says: No Littering! You can get a bottle if you fish on the right side of the bridge that is near that sign. Its darker water than normal.
Unlike other Zelda games (where you got attacked if you hit the Cuccos), in Twilight Princess if you hit a Cucco about 8 times, you'll be able to control it for a short period of time.
L-target and perform four sword thrusts by tilting up on the control stick and pressing B. Make sure to leave enough room so only the fourth thrust connects. The Darknut will then swing its sword twice; immediately after the second swing, perform a Jump Slash on the Darknut. This will cause the Darknut to raise its sword in the air, leaving you free to attack it.
In the final boss battle, cast the fishing rod to distract him and get in a few easy hits.