It's not just a problem with Skype, I believe it's a problem with, you've guessed it, PulseAudio.
Workaround? Indeed there is.
Disabling PulseAudio's Glitch Free Audio seems to have solved the crackling for me (which became unbearable on my Ubuntu 12.04 64 bit)
To do this, edit the /etc/pulse/default.pa file in your favourite text editor.
Search for the following line:
load-module module-hal-detect
and append "tsched=0" to the end:
load-module module-hal-detect tsched=0
restart pulse (or just reboot your system), and the crackling should be gone.
Not sure what the side effects are by disabling Glitch Free Audio, but I can't seem to find any yet.
This helped me, I hope will work for you as well:
If you don't have a line with load-module module-hal-detect, then search for following line:
load-module module-udev-detect
and append "tsched=0" to the end:
load-module module-udev-detect tsched=0
restart pulse (or just reboot your system), and the crackling should be gone.
I found this info here.