It seems this bug doesn't apply to me, and that I just needed to find the  right
documentation, then set the model= parameter.  Sorry for the waste of time.

I'll note my solution in case it helps random web searchers, but it's NOT
related to this bug.  I should also qualify these hints: I just found something
that worked for me and don't deeply understand what is going on.

== 
The document with the hint required was ALSA-Configuration.txt's
"Module snd-hda-intel" section, online at:
  http://www.kernel.org/doc/Documentation/sound/alsa/ALSA-Configuration.txt
or /usr/share/doc/alsa-base/driver/ALSA-Configuration.txt.gz locally.
(It's mentioned in https://help.ubuntu.com/community/SoundTroubleshooting)

I set the option in a new file (/etc/modprobe.d/alsa-hda-intel-model.conf):
  options snd-hda-intel model=6stack-dig
(the first one I tried worked with my headphones, that's all I need)

I applied the change with:
$ sudo alsa force-reload # BEWARE kills you're audio using processes
$ cat /sys/module/snd_hda_intel/parameters/model

This fixed the stutters/crackles at high volume for via both alsa and
pulse.

I've since discovered the excruciating details:
http://www.kernel.org/doc/Documentation/sound/alsa/HD-Audio.txt
http://www.kernel.org/doc/Documentation/sound/alsa/HD-Audio-Models.txt

(Things that didn't help: 
* Jaunty proposed kernel (I think I already had the patches discussed above)
   2.6.28-15-generic #52-Ubuntu SMP Wed Sep 9 10:48:52 UTC 2009 x86_64 GNU/Linux
* snd-hda-intel position_fix parameter, description sounded relevant though)

-- 
Crackling / scratching noise using Pulseaudio
https://bugs.launchpad.net/bugs/345627
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