I'm also experiencing audio stuttering and wanted to contribute my
findings.  I'm using Ubuntu 8.04 with the rt kernel.

First off, I think there are many sources of this problem which all
result in audio drop outs, which is likely why this bug has become so
confusing.  I was also experiencing various issues with PulseAudio, so I
have completely disabled it and am now using ALSA dmix.  For this
reason, I should probably be filing this under another bug, which I will
do as I gather more information.

In my case, the audio drop out issue does not occur with applications like 
MPlayer, Amarok and aplay.  I also tried VLC, which suffers very slightly from 
this issue (which I suspect is another issue).  Rhythmbox, Totem, and Sound 
Recorder on the other hand are really bad.  Minimizing/maximizing windows 
causes a rather large audio drop out about 50% of the time.  This lead me to 
believe there is something wrong with gstreamer.  So I decided to try 
gst-launch:
gst-launch-0.10 filesrc location=test.mp3 ! mad ! audioconvert ! audioresample 
! alsasink

Indeed, this gstreamer pipeline has the same audio drop out behavior as
all the other applications using gstreamer.  I also tested ogg files
with a gst-launch pipeline, with the same poor results.  So in this
case, I think I am experiencing some issue involving gstreamer.  I'll be
sure to post any more info as I discover it.

-- 
Over-optimistic buffering in PulseAudio causes underruns (audible stuttering, 
pops)
https://bugs.launchpad.net/bugs/190754
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