It doesn't look like the problem is in pulseaudio though.
I have the very same problem (buffer underruns in alsa and the resulting 
stuttering / crackling), but the issue not only occurs when I use Pulseaudio.

It's a generic issue with all applications which access Alsa, although
varying the size of the buffers in pulseaudio can reduce the interval of
stutters.

For me it's not the Wifi driver which is causing the issue, but (i think) 
something in the graphics driver since I get the stuttering whenever large 
bitmaps get drawn on screen.
This seems to be highly dependent on the hardware and there appear to be 
multiple hardware configurations which can trigger the underruns in Alsa.
I can e.g. trigger it reliably by switching the video renderer in VLC from GLX 
to Xvideo and back and it will start stuttering as soon as the Xserver is under 
load. Switching between Pulseaudio and Alsa (direct, PA suspended) as audio 
backend makes no difference at all, well except that the interval of the cracks 
is directly related to the buffer size used by the corresponding applications.

What would be noteworthy, this issue is rather new for me.
There appears to be some regression in the Alsa driver which makes it less 
tolerant towards long running, non-interruptible service routines from other 
drivers.

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https://bugs.launchpad.net/bugs/1045771

Title:
  Underruns and stuttering

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