The AdditionalExternalJavaScriptFunctions element could be put in the first filter XSLT.

Example

Example of embedding tinyMCE (a famous Javascript WYSIWYG Editor) into Plex-XML.
RichTextEditor

<xsl:template name="additionalExternalJavaScriptFunctions">
 <additionalExternalJavaScriptFunctions>
  <script language="Javascript" type="text/javascript" src="jscript/tinymce/jscripts/tiny_mce/tiny_mce.js"/>
 </additionalExternalJavaScriptFunctions>
</xsl:template>

<xsl:template name="additionalJavaScriptFunctions">
 <additionalJavaScriptFunctions>
  tinyMCE.init({mode : "textareas",theme : "simple",cleanup : true});
  Event.observe($('FooForm'), 'FooForm:submit', function(){tinyMCE.triggerSave();});
 </additionalJavaScriptFunctions>
</xsl:template>