By collecting all of the Stray Fairies and returning them to their respective Fountains, the Great Fairies will reward you with various upgrades.

Reward	How to unlock
Charged Spin Attack	Collect all the Stray Fairies in the Snowhead Temple and return them to their Fountain.
Defense Boost (Damaged Reduced By Half)	Collect all the Stray Fairies in the Great Bay Temple and return them to their Fountain.
Double-Sized Magic Meter	Collect all the Stray Fairies in the Woodfall Temple and return them to their Fountain.
Great Fairy Sword	Collect all the Stray Fairies in the Stone Tower Temple and return them to their Fountain.