I was recently able to fix choppy skype audio and restore the previous state of my n900 by doing:
sudo kernel-config load ideal
sudo kernel-config default ideal

The audio chop is thus likely affected by:
kernel-config

By simply tuning the frequencies, voltages, etc. the chop can be increased and decreased.

This is evident by running:
sudo kernel-config load ideal
and doing a skype test call to echo123
And then running:
sudo kernel-config load myprofile
(where myprofile could be whatever settings)
and doing a skype test call to echo123 again to compare audio chop
This can be repeated until a suitable kernel-config is found.

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More info:
Not sure if this fix is specific to my phone. Skype still has occasional chop glitches but they are no longer significant enough to distort audio to a point where I can not understand or it is not usable.

The maemo overclocking wiki commands are what I was using with "myprofile" are listed at:
http://wiki.maemo.org/Overclocking#Overclocking
http://wiki.maemo.org/Overclocking#Undervolting
ie) myprofile
sudo kernel-config load default
sudo kernel-config limits 250 900
sudo kernel-config save myprofile
vi /home/user/.kernel/myprofile
SMARTREFLEX_VDD1=1 SMARTREFLEX_VDD2=1
sudo kernel-config load myprofile

Ironically the settings on the wiki seem to improve everything on my n900 with the exception of making more chop on skype (on my side only) as well as decreased audio volume to on the handset I am calling. I can even play video again without reboots/instability.

Going with the n900 default settings and no overclock seemed to be too slow to go back to and I haven't necessarily noticed any improvement to skype chop using:
sudo kernel-config load default

Hope this helps someone. Also, this phone is 3 years old already!