I’m running Snes9x and there’s the occasional audio hitch / crackle, and I’m running a 6700k. I’ve tried increasing the audio latency (up to 96) but don’t think it helped.
Am running v-sync, with Hard GPU Sync off (though I had that on before - no difference).
You can try increasing the dynamic audio rate control value in settings > audio.
There is no such setting for me in 1.5.0 
make sure you have enabled ‘show advanced settings’ in settings > user interface.
Great, done that and increased it from .005 to .007 - should that suffice? Any downsides to this?
Dunno, just increase it until the pops go away. The only downside is that it can make your audio sound warbly if you set it too high. The default setting is below the threshold of human detection.
Hmm, some pops are definitely caused by music / sound effects beginning playback. I wonder if this is a problem with the core.
It seems better with Audio Sync disabled. Will test further.
Maybe you could try setting your CPU to a higher performance rate when idle, through power options. I think the default is 20%? Try a higher number or disable it alltogether.
Also, can i ask, why not using BSNES instead? Since you have a powerful system, i don’t see a reason using SNES9x and not a more accurate emulator that probably won’t cause your CPU to go idle.
BSNES didn’t support cheats at all until a week or two ago, and I don’t think it supports the full range of cheats.
The most noticable pops (and they are quite quiet actually) is definitely at the beginning or end of a sound effect or music track. Not all, but some.
I will look into your suggestion, but it doesn’t feel like processor problem because it’s just a little pop at the beginning or end of some sound effects / music. However, I did just check my power profile and the minimum CPU rate is 5%. Is there a good way of watching the processor speed while running RetroArch?
EDIT: by the way I tried BSnes and I get the same occasional popping, usually at the start / end of a sound effect / music track. Doesn’t Snes9x share a lot of code with BSNES?
No, they don’t share any code. Latest Snes9x has an APU core written by byuu but it’s not the same as the one used in bsnes.
Hmm, just tried on my headphones and there’s no popping - it’s only on my USB speakers.
I found a part of a game where I can reproduce the problem every time, it’s here: https://youtu.be/8gta3sNOiWM?t=27m43s
The pip-pip sound without any music causes major popping, but only on my USB speakers. What the heck.