- On Windows/Mobile you set this registry key (HKEY_LOCAL_MACHINE/SOFTWARE/Skype/Phone/Audio/DisableCodecs) to contain the codec's you don't want Skype to use (e.g. for Pocket PC you might want to disable higher CPU codecs: "ILBC G729 EG711U")
- On Linux/OSX you add the disabled codecs inside these tags: <DisableCodecs> <\DisableCodecs> in the config.xml file (usually found in ~/.Skype/your_skype_username/config.xml). They need to be put into the (usually existing) <Call> tag which is within the <Lib> tag.
- Furthermore you can actually force the use of a particular codec by using the <ForceCodec> tag/Reg key in the relevant place.
There's also other fun stuff you can tweak - like adding a <video> section and make Skype use a particular resolution (you'll need to convert this to an appropriate Registry entry on Windows):
For an interesting read on Skype see columbia.edu, and for papers on performance see Politecnico di Bari and Politecnico di Torino.
[Updated: 16mar2012: More on location of Codec config tags]