This is caused by a bug in the sound system in Karmic, that tries to power the sound card down every ten seconds to "save power", and the click is that failing.

So, to fix it, turn off the soundcard powersave feature.

Edit /etc/modprobe.d/alsa-base.conf , for example with nano:

sudo nano /etc/modprobe.d/alsa-base.conf

or graphically:

gksu gedit /etc/modprobe.d/alsa-base.conf

In that file (likely at the end) there is something similar to:

# Power down HDA controllers after 10 idle seconds
options snd-hda-intel power_save=10 power_save_controller=N

Comment out the final line, like this:

# Power down HDA controllers after 10 idle seconds
#options snd-hda-intel power_save=10 power_save_controller=N

Now restart the computer (logging off and back on wasn't enough for mine). Then try playing a sound, and listen for the clicks afterwards. Should be gone, hopefully!