In regards to audio popping when paying back audio I've tried many things with no success except using an external USB audio interface. I finally took it to the Apple store and they said it was the audio controller. They said it may be related to the optical digital output getting stuck when headphones are unplugged. Their solution was to replace the logic board under AppleCare. I got my Mac back and the problem is gone.
As a side note, I have been quite impressed with the audio quality from the built in audio. Both the line in and out have a signal to noise ratio of less then -88db RMS and has a frequency range of at least 5 – 20kHz. That's to the extents I tested. The actual signal to noise ratio is less than (better than) -88db, I tested it by running the output of silence directly into the input. The noise of both the input and output added together is -88db.
Also the MacBook Pro 17" doesn't have any internal analog interference to the audio in and output. With other Apple laptops, iMacs, and the Mac Pro I have noticed varying amounts of noise caused from the CPU or even the USB bus. For example, hearing a buzzing whenever the mouse is moved or a page is scrolled. A work around for that issue is if you have the audio output plugged into an amplifier or external speakers, turn your Mac's volume all the way up, and turn down the external amp or speakers to your desired level. Also make sure the format in the "Audio MIDI Setup" is set to 24 or 32 bit for the output, this setting should always be at the highest setting.
Hopefully this will be helpful to everyone.
MacBook Pro 17"
2.66GHz Intel Core I7
4GB Memory
Mac OS X 10.6.8
The audio card is "Intel High Definition Audio"