This document includes fast examples to use @mbabker's method to use the media folder to allow stylesheets and javascript overrides:
I have also added the method to use overridable images in the media folder.
JHtml::image('mod_transformer/printer.png', JText::_('JGLOBAL_PRINT'), null, true, false);
Checks in this order:
/templates/MY_TEMPLATE/images/mod_transformer/printer.png
/media/mod_transformer/images/printer.png
JHtml::stylesheet('mod_transformer/transformer.css', false, true, false);
Checks in this order:
/templates/MY_TEMPLATE/css/mod_transformer/transformer.css
/media/mod_transformer/css/transformer.css
JHtml::script('mod_transformer/transformer.js', false, true);;
Checks in this order:
/templates/MY_TEMPLATE/js/mod_transformer/transformer.js
/media/mod_transformer/js/transformer.js