DTS-HD Master Audio / Dolby TrueHD / PCM 5.1

Manta-
You listed them in the order of my preference.

As far as your DVD player, the audio will sound best through the coax or toslink, not the HDMI. Your Bluray player will however sound best when playing the high-rez formats (and only make sound)through the HDMI. If your watching a bluray with only standard DTS/DD soundtracks it may be worthwhile to A/B with a Toslink/Coax and see which sounds the best to you.

I have the Pioneer Elite BDP-05FD and I am confused about the HDMI Audio Out part of the setup. Right now, I have it setup to AUTO because I wanted to hear DTS-HD Master Audio. If I set it to PCM, do I still get better quality of sound from DTS-HD Master Audio?

PCM will remove DTS-HD Master Audio and Dolby TrueHD and revert to the older DTS and or Dolby Digital formats.

07-28-09: Drewmb1
PCM will remove DTS-HD Master Audio and Dolby TrueHD and revert to the older DTS and or Dolby Digital formats.

Not true unless the player lacks the ability to decode these formats. IIRC, this player can do both with a firmware update. The only other exception is if the user enables "secondary audio."

In any case, to get back to the OP's original question: There is no general preference, imho, as they are all lossless full-bandwidth channels. The mastering may be somewhat different in some cases leading to a specific preference but that is not generalizable.

Kal