I have found the temporary "solution" until Apple diagnoses the root cause and creates a fix. After spending some time with an Apple support tech who did a remote log-in session to my early 2011 MacBook Pro 15" so he could see what was going on, we determined the issue causing the audio problem is caused by SLEEP mode. Whenever you leave your MBP on and close the clam shell (lid) or let it go into sleep mode when open, when you re-awaken it and then launch FaceTime and initiate an audio or video call the audio "popping and clicking" issue occurs. I have reset the PRAM, I have changed Wifi, I have switched from the internal Bluetooth 2.1 adapter to an external Bluetooth 4.0 dongle via Bluetooth Explorer app, I have killed the core audio process, re-loaded a fresh copy of OS X 10.10.1, reset the SMC, started iTunes and then played a song, and used both BT headphones and plug-in jack headphones. Most of these "fix" the issue until it returns again when the MBP exits SLEEP mode. It also explains why re-boots fix the issue.
I can consistently make it NOT happen by keeping my MBP out of sleep mode when plugged in and never closing the lid when it is on. I do a full shut-down and boot-up each morning when I want to use it and have set the ENERGY SAVER mode under SYSTEM PREFERENCES to "Never Sleep" when my MBP is using the Power Adapter. I can make the problem consistently re-appear by putting the ENERGY SAVER settings back to default and let the MBP go into sleep mode or closing the lid for 15 seconds or more then opening it. The Apple tech set up a Test administrator account to see if the issue was with my account settings. Sure enough, the minute we put the MBP into sleep mode the issue came back. He has documented all this and forwarded it to Apple development engineering. It is obviously a bug in the Yosemite software and why it seems to happen with more frequency for owners of 2011 MBPs is beyond me. My late 2014 MacBook Air doesn't seem to exhibit this problem but I don't use it daily like my 2011 MBP.
Not the "fix" we are all looking for but I am pretty confident it at least defines the root cause scenario and how to avoid it until there is a fix from Apple :-)