Sound Quality: difference in digital outputs? optical vs coax? discrete vs integrated?

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In short, I'm looking for the best stereo sound I can get from my
Linux system---the main use will be listening to my CD collection
(ripped as FLAC).

A specific question: if using digital output, is there a difference
(sound quality-wise) between optical/toslink and coaxial?  Say my
soundcard can output both via optical and coax, and my amp also
supports both inputs: any reason to choose one over the other?

Also, if I'm looking at pure digital output, is there a quality
difference between sound card models?  My understanding is quite
naive (and certainly incomplete!) but it seems like if the software
(flac123, mpd, whatever) converts the FLAC code to a digital audio
signal, the sound card doesn't really have any work to do.

In other words, my motherboard (Abit IP35 Pro) has an optical SPDIF
output for its Intel HD Audio system.  Would this be any
better/worse than, say, a Chaintech AV-710 with optical out (which
I'm using in another PC), or an MAudio Audiophile 2496 coax SPDIF
output?

My understanding has always been that "digital is digital", but
after doing some reading today, I'm not so sure that's true.

In general, in addition to answering the above questions, I'm kind
of looking to continue this thread I found, "Best card for
bitperfect SPDIF I/O": 
http://www.mail-archive.com/alsa-user@xxxxxxxxxxxxxxxxxxxxx/msg21140.html

Some general comments/open-ended questions:

    - I have an MAudio Audiophile 2496.  I was using its analog
      (RCA) outputs to an amp, and then on to some speakers.  I
      noticed a crackling sound in one of the speakers---I've
      literally changed everything after the sound card (cable,
      amp, speaker wire, speakers) and the crackling persists.  So
      either I have a bunk card or there's too much RF noise in my
      case.

    - I switched back to the onboard Intel HDA chip, and am using
      its analog output.  I *thought* I heard a little bit of
      crackling last night (but I need to do more listening to
      verify this).  Certainly the analog sound from the integrated
      chip isn't as good as the MAudio (crackling aside).

    - It is for the above two reasons that I am looking at going the
      digital route---if my case is internally noisy, shouldn't
      digital avoid these problems?

    - In general, are there any Linux "audiophiles" out there (i.e.
      using your Linux system as your audio source)?  How do you get
      the signal (analog or digital) out of the computer and into
      your amp?

Thanks,
Matt


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