I think I found a secret (spoiler-free!)

[Shank]

If you fly high above the Lumpy Pumpkin and then hop off your Loftwing, these rainbow-colored... bugs, I guess, start falling with you. If you move around from side to side and collect them all (I couldn't count them, but there are about ten or so) then you'll get rupees! I think I got 20 Rupees, but it might be dependent on which color bug you pick up last? Maybe? I dunno.

I've never heard anyone mention this before. Has everyone been holding out on me or something? Have you found any other secrets?

[Link8150]

I have never heard of or seen anything like this, though it does sound very interesting so I'll have to try this.

[balloondude2]

I've done that once, I didn't think much of it. I think it happens in a few other spots too, but I can't remember. Most the time, I would only be missing one or two of the "things" before I hit the ground.

[Shank]

I think it happens in a few other spots too

Yeah, I found them over one other island, too. From far off they look like a bunch of skydivers falling in formation. As you approach them, they break apart, presumably so they can fall in formation with you.

[kram1032]

One of the characters actually tells you about that. - Either in the Bazar or in the Lumpy Pumpkin. Not quite sure...
I tried it out above the Lumpy Pumpkin but failed. So you need to fly very high for this? Well, that might explain my failure.

[Emhave]

I've done this many times and I'm pretty sure the award is 20 rupees each time. As you guys already mentioned, they also appear above the island that looks like a volcano, where you can actually fall into the "crater" of it. There is a Goddess Chest hidden here as well.

[WolfLink]

This game has seemed really cool so far. It's a shame I haven't gotten to play it much. I am going to have to try this out next time!