I just had good success with adding a parameter to /etc/modprobe.d/alsa-
base.conf:

options snd-hda-intel position_fix=1

I got the idea from:
  http://ubuntuforums.org/showthread.php?t=843012

And the file located at:
  /usr/share/doc/alsa-base/driver/ALSA-Configuration.txt.gz (use gunzip to 
unzip it)

The section on snd-hda-intel contained the following:
     Note 2: If you get click noises on output, try the module option
            position_fix=1 or 2.  position_fix=1 will use the SD_LPIB
            register value without FIFO size correction as the current
            DMA pointer.  position_fix=2 will make the driver to use
            the position buffer instead of reading SD_LPIB register.
            (Usually SD_LPLIB register is more accurate than the
            position buffer.)

My current configuration: Ubuntu 8.10, alsa 1.0.20, pulse audio 0.9.10,
using equalizer via ladspa

Pulse audio configuration files attached.

The module parameter appears to be extremely important.


** Attachment added: "daemon.conf"
   http://launchpadlibrarian.net/26728537/daemon.conf

-- 
Crackling noise after update to pulseaudio
https://bugs.launchpad.net/bugs/301755
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