Cool Edit has a scripting language to auto task a lot of the features. So instead of manually doing a lot of stuff you can write a script to automatically do a lot of the work for you instead of you having to do it yourself. Like I got away I do Isotonic tones and Binaural Beats with Audacity but it is a drawn out process to incorporate both in the same sound file. I think if Audacity had a scripting part it would make the process a lot less tedious.
Audacity has an extremely powerful scripting language built in. It is called “Nyquist”.
Short commands may be run in the “Nyquist Prompt” effect (http://manual.audacityteam.org/o/man/nyquist_prompt.html), or you can even create full-blown plug-ins (http://wiki.audacityteam.org/wiki/Nyquist_Plug-ins_Reference).
There’s about a hundred user contributed Nyquist plug-ins on the Audacity wiki: http://wiki.audacityteam.org/wiki/Download_Nyquist_Plug-ins
and many more “experimental” plug-ins on these forum pages: http://forum.audacityteam.org/viewforum.php?f=42
For questions / discussion about Nyquist scripting, see this forum board: http://forum.audacityteam.org/viewforum.php?f=39
Audacity also has “Chains”. See: http://manual.audacityteam.org/o/man/chains_for_batch_processing_and_effects_automation.html