Rupees or Bees
This requires a bit of luck, you either get some Rupees or end up with a swarm of bees chasing you. All you have to do if you have the Pegasus Boots is run into trees that are not connected with other trees and wait to see if you get Ruppees or Bees.

Silver Keys:
These become unlocked when you complete each level with a team score of over 1,000 Rupees and have defeated Vaati.

Gold Keys:
These become unlocked when you complete each level with a team score of over 3,000 Rupees and have defeated Vaati.

Hero Keys:
These become unlocked when you complete each level with a team score of over 5,000 Rupees and have defeated Vaati.

Defeating Giant Warriors:
If you have a Roc's Feather jump over the Giant Warriors when you are
battling them and press B for an instant kill.

Shadow Battle Bonus Arenas:
To unlock the last five Shadow Battle Arenas successfully complete the
Hyrulean Adventure.

Boomerang:
Obtain out of reach Force Gems and other items by using the Boomerang.