Pokemon Emerald, go to a region you can change the route easily (i'm testing in route 118 / 123), you'll notice some noise in the transition

You can notice too in the Continue screen, when the music is ending/fading

I have similar clicking issues in the Pokémon Crystal intro. At the beginning, you hear a clicking/crackling noise when the Unowns appeared, and also during the Gamefreak logo. Basically, you hear a popping noise everytime a quite short sound is played.

I uploaded a video showing the issue to Youtube:

https://www.youtube.com/watch?v=X4nfbHO1aoc

Please also note that I think that there's a sound issue during the Pokemon intro. When the grass moves the second time [at 0:20 and 0:21], it seems that the sound of the second grass movement is wrong. I have to verify this with another emulator.

Yep, the pops are exactly what I'm experiencing.

This may be a duplicate of #461 . If you change the FPS target to 60 instead of Native (59.7), do the pops become much less frequent?

My FPS target is already set to 60. I changed it to 59.7, and the pops are just as frequent.

Same here. No changes between 59.7 and 60 FPS.

Take note please: At some point my PC stopped behaving differently on different FPS settings. For whatever reason (hardware change? Sound options change? Don't know...). Now both settings pop the same as the 60 FPS setting did before (and it was the option with less popping). Which is not too bad, but still noticeable. I still use the Mother 3 title screen for testing.

Can you try bisecting this?

It started with 8ac6f83

Audio popping is coming from PSG channel 1. It makes a pop every time it plays a note.

Note that this fixes many but not all of the audio issues with Crystal. And yeah the grass effect sounds wrong to me, but I haven't confirmed it yet.