Default systems files are delivered in the GSM format. In order to improve the quality, you must source all those files and replace them.
There are two types of sounds:
Default prompts come in all needed formats (ulaw, alaw, gsm, g729) to avoid transcoding. (Look under System -> Sounds to change the format)
The quality of these sound files is easy to test:
Make an extension and force its codecs to 'gsm'. Dial *123 and browse the prompts. Now edit the extension and force codec 'ulaw' or 'alaw' (disable all other codecs). Dial *123 and you will notice the difference.
This should be done with a standard hardphone (such as Polycom) rather than a softphone on a PC.
If you want to upload a new prompt/greeting, you should use the 'Sound Converter Wizard' which will convert a high quality WAV to a set of native formats in the PBX.
There is only one case in which the prompt is only 'gsm' and that is when you create it with the phone (but that will be of poor quality anyway).