There is problem to load jQuery plugins which require some configuration in jQuery namespace before loading of js file. As an example I will use jqGrid library.

Following code will not work, because jQuery() will render always files before embeded scripts and we need to set useJSON before jquery.jqGrid.min.js, but after grid.locale-en.js.

echo $this->jQuery()
    ->addJavascriptFile($jqgridLibPath . '/js/i18n/grid.locale-en.js')
    ->addJavascript('jQuery.jgrid.useJSON = true;')
    ->addJavascriptFile($jqgridLibPath . '/js/jquery.jqGrid.min.js');

With Zend_View_Helper_HeadScript I could do following:

echo $this->headScript()
    ->appendFile($jqgridLibPath . '/js/i18n/grid.locale-en.js')
    ->appendScript('jQuery.jgrid.useJSON = true;')
    ->appendFile($jqgridLibPath . '/js/jquery.jqGrid.min.js');

1. Solution could be to change the rendering order to comply with Zend_View_Helper_HeadScript, so it will mix embeded and loaded Javascript in order it was added.

2. Other solution could be to add function like addJavascriptBetweenFiles() and only that would keep the order:

echo $this->jQuery()
    ->addJavascriptFile($jqgridLibPath . '/js/i18n/grid.locale-en.js')
    ->addJavascriptBetweenFiles('jQuery.jgrid.useJSON = true;')
    ->addJavascriptFile($jqgridLibPath . '/js/jquery.jqGrid.min.js');