Where are the places I can find fairies for my bottles?

I've seen fairies in random places, but some of them don't replenish after getting them? Where are the places I can find fairies repeatedly?

There is a spot right outside the Fire Sanctuary, in the caves with the frog mouths, with a burrowing hole. It's a convenient spot since you can come from the sky and drop in to the bird statue nearby. When you burrow in that hole and come out the other side, there is a cave with a heart piece and a bunch of fairies flying around. However, you need the Mogma Mitts in order to burrow into a hole. But you can keep going back there over and over after you get the heart piece to get more fairies.

Places where fairies naturally spawn in the world will always spawn in the same area after some period of time (my theory, after defeating a dungeon). This is in the Normal Mode and in Hero Mode. Having to go back to these locations to get them can be inconvenient so you should consider alternate ways of getting fairies.

The easiest way to get three free fairies would be to draw a Triforce on a Goddess Wall. Though you would first have to find a Goddess Wall and they can only be used every once in a while after some period of time (same theory).

A much more convenient way to get fairies IMHO would be to use Glittering Spores on regular hearts to transform them into fairies. You'll need an extra bottle to get and hold the Glittering Spores but you get five servings of the stuff when you get it giving you potentially five fairies. Hearts are much more easier to find in general so fairies will be easy to find too by extension.