I ran across hearing this sound recently as part of my long going journey to fix the problems that began after the dealership replaced the wiring harness (what a fiasco).
I've searched the forums and have run across a couple of threads that mentioned this same behavior so I know I'm not crazy.
But...none of the threads ever mentioned what the fix was or even what the cause turned out to be. Best I can tell, it's some kind of backfiring coming back out the intake. It's very quiet but defintely noticeable if you remove the cover of the air filter housing or even pull the IAT out of the air filter housing.
The reason I'm even trying to diganose the problem is because I have what appears to be a growingly common problem with light acceleration stumbling and wonder if this noise might be related.
I've recently replaced all the plugs and gapped them (2x Plat. Autolights) and replaced the plug wires. EGR passages cleaned, TB cleaned, and just ran a can of Berryman's intake cleaner (nice little kit with a hose that siphens the fluid out of the can. I just reset the PCM and will see if anything has changed.
Oh...and while I've got the thread going, I'm having what seems like classical IAC valve issues. I just did the cleaning on it with TB clener (wasn't really all that dirty looking). Doesn't seem to have made ANY difference. Just trying to avoid spending $80 on a new one.
I'm going to do a full UI/LI cleaning along with all the seals/gaskets, new injectors, and fuel pressure regulator (basically a 120K mi. spring cleaning) this spring after it warms up some.
In the meantime, c'mon guys! I know I've seen threads where a couple others have heard this popping sound too. Just hoping to maybe hear the results of those cases.