This for all of you Joomla! 3.2 Template developers out there. Yes, you.
Here’s a snippet of code (shoutout to this Joomla! Forum post) that we use in some of our templates to remove unwanted JS files:
//Remove MooTools unset($doc->_scripts[JURI::root(true) . '/media/system/js/mootools-core.js']);
Just be sure that this code is somewhere before your <jdoc:include type=“head” />.
To remove them, create an override in your template and remove the line. Obviously, this will make certain functions in the module, well, not function.
Also, one more word of caution: DO NOT MODIFY CORE JOOMLA! FILES. One of the benefits of using Joomla! is output overrides—using overrides will prevent you from overwriting files that could potentially change when the site gets upgraded to a newer version of Joomla!.