Eastern Fairy Island

Visit this small island with the seashell on top when you've gotten Bombs.

Blow up the rock blocking the entrance and enter the shell. The Great Fairy will appear and upgrade your maximum carrying capacity (typically for Bombs at this point in the quest).

Come back to this island later when you're trying to complete the tree spirit sidequest.

Look for a platform northwest of the island. It's worth a visit just to steal Joy Pendants from the watchers -- and if you take out all three, a treasure chest with a Boko Baba Seed will appear.