PulseAudio is the default audio interface in Ubuntu. Somehow I managed to get it working with a reasonable latency (35msec — which isn't perfect, but it's a built-in Intel sound card — and no overruns).

PulseAudio

pulseaudio --high-priority=1 --daemonize=1 -n -F $HOME/.jackd.pa

~/.jackd.pa:

load-module module-jack-sink
load-module module-jack-source

JACK

/usr/bin/jackd -R -P10 -t5000 -dalsa -dhw:0 -r44100 -p512 -n3 -m

Set "Periods/Buffer" to "3" and Timeout to "5000", following the advice of a Renoise forum thread. Setting "Frames/Period" to 256 reduces the latency to 17.5msec, but is spoilt by a few occasional overruns.

ALSA

pcm.pulse {
    type pulse
}
ctl.pulse {
    type pulse
}

asoundconf set-pulseaudio
asoundconf set-default-card Intel

/etc/modprobe.d/alsa-base.conf:
options snd-hda-intel position_fix=1 model=auto

Linux Realtime Kernel (linux-kernel-rt)

HDA Intel card (Realtek ALC883)

See also: JACK diagram; JACK FAQ; PulseAudio perfect setup.

RealPlayer crashes with PulseAudio, but you can run it as aoss realplay and set it to use OSS for output as a workaround.

For Skype, "set “Sound Out” and “Ringing” to the “pulse” device, and set “Sound In” to the hardware definition of your microphone."