Comment 9 for bug 234004

Update.
The reason for stuttering is native PulseAudio plugin in Audacious.

If you select ESD plugin (which is automatically fetched and emulated by PulseAudio) as output in Audacious, it will play WAV gapless!!!!

As told on pulseaudio page: "set buffer size to 300 to prevent stuttering when playing MP3 files"
http://www.pulseaudio.org/wiki/PerfectSetup

However, we have WAV issue AND it doesnt help... even increased it to 3000, no help.

I experimented a little more:
Setting output to ALSA plugin(which is fetched by PA also, if you modify /etc/alsaconf) temporary corrects the problem too.
And, Alsa plugin has a default buffer of 500, same as default buffer for Pulse plugin.