They can upgrade your armor! Not only that, but if you have a full set of any armor, they can sometimes imbue them with special properties and effects, such as decreasing the stamina for charged attacks or making you entirely resistant to fire.
If you have not been introduced to Great Fairies in The Legend of Zelda: Tears of the Kingdom (or you don’t know about them from Breath of the Wild), you’ll want to find them as soon as you can.