Yep, mine does it too in Netflix. I just started a thread about it in this forum. Also, just found this in the D3 forum..
http://forums.androidcentral.com/motorola-droid-3/106904-netflix-audio-clicking.html
It doesn't seem to just be netflix though. Pandora does it as well...just not as easy to reproduce.
I noticed the crackling in my speakers but it only when LTE is in use. I switched it to CDMA only and haven't had any issues.
Obviously not a solution but narrows down the problem, at least for me.
Larry