As crazy as it may seem, reducing the buffer may help. Also I noticed
reduced CPU usage when I manually set the sample rate to my soundcard's
native rate, 48000Hz.

Try changing your /etc/pulse/daemon.conf to reflect the following
changes:

; default-sample-format = s16le
default-sample-rate = 48000
; default-sample-channels = 2

default-fragments = 8
default-fragment-size-msec = 10

This has eliminated stuttering for me with both ICH4 and ICH5 (AC'97)
cards, but it may vary for other soundcards. Perhaps some AC'97 based
cards have a small buffer, hence if the fragment number or fragment size
is too high, it cannot fit in the buffer...

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