Not sure if this is helpful at all, but I all of a sudden experienced this over the weekend (which worried me given I just dropped ~5K on a new MBP 15 and I'm a music producer).
I read a few forums and followed the recommended approaches and suggestions but at the time it didnt make a difference.
Randomly as it started, of of yesterday it has not had a problem nor recurred. I havent rebooted (
8:40 up 17 days, 14:33, 3 users, load averages: 2.44 2.37 2.26) since I last set it up and so problem has gone away as fast and randomly as it came.
Trying to retrace my activities - only thing I've done is installed new software but none of it (AKAIK) were anything that would touch sound libraries, drivers, config settings. etc.
Interestingly though, and to my relief, I did use an external sound card once the problem started to check that it was limited to something on the internal sound board/controller, and where at the same time the cracking and popping could be heard through internal speakers, nothing of the kind was heard through an external sound card. Doesn't give way to many clues other than its a different driver (ASIO based sound driver) etc.