It's definitely a 10.4.10 problem, and never happens during playback. I just stopped iTunes and about a minute later there was this "pop" (mostly a slight low thud from the Subwoofer). When I start iTunes back up I get it again just before the music comes in.
This is with external speakers plugged in - i've tried but can't hear it with the internal ones...but since it's a very low sound I didn't expect to.
This "popping thing" is kinda strange. I'm left wondering if it's not limited to just desktop speaker systems since everyone in the thread seems to mention "speakers", etc.
I've worked on a couple of audio projects today on my C2D Macbook, and I happy to say it's not happening on my system...
but... I rarely have any reason to monitor from the analog audio output jack on the Macbook. I use a FireWire device for that, and it's as clean of pops and clicks as it was before 10.4.10.
So, just to see... I plugging a set of Sony V7000J headphones directly into my C2D Macbook's headphone jack I'm not hearing any pops at all. This is after staring iTunes, exiting it, and then wearing the headphones for 3 minutes after iTunes was stopped. On restarting iTunes and playing a tune I don't hear a click, pop or or any sudden bursts of noise, etc. The Sonys go down to 5Hz and are efficient enough to crank up to the sound levels loud enough to cause pain off the Macbook's output, so I'd think the pops would be audible...
I don't have a pair of 'consumer' desktop speakers where I'm out to try out right at the moment. But hooking up an adapter from the Macbook's audio jack to a set of Lo-Z cables run straight into a 800 watt power amp connected to a couple of 15" 2-way speakers I don't get any pops after trying the same test at volume levels high enough to shake the floor joists.
Is it possible the desktop speaker system you're using has some sort of circuit built in that automatically cuts the speaker system off after a certain period of no audio input that's perhaps the source of these pops?