This is just a modified version of the function Mage_Adminhtml_Model_Email_Template::getSystemConfigPathsWhereUsedCurrently() and it returns all the used email templates configuration paths

gistfile1.txt

    /**
     * Collect all email templates system config paths
     *
     * @return array
     */
    public function getEmailTemplatesSystemConfigPaths()
    {
        $paths = array();

        $configSections = Mage::getSingleton('adminhtml/config')->getSections();

        // look for node entries in all system.xml that use source_model=adminhtml/system_config_source_email_template
        // they are will be templates, what we try find
        $sysCfgNodes    = $configSections->xpath(Mage_Adminhtml_Model_Email_Template::XML_PATH_TEMPLATE_EMAIL);
        if (!is_array($sysCfgNodes)) {
           return array();
        }

        foreach ($sysCfgNodes as $fieldNode) {
           $groupNode = $fieldNode->getParent()->getParent();
           $sectionNode = $groupNode->getParent()->getParent();

           // create email template path in system.xml
           $sectionName = $sectionNode->getName();
           $groupName = $groupNode->getName();
           $fieldName = $fieldNode->getName();

           $paths[] = implode('/', array($sectionName, $groupName, $fieldName));
        }

        return $paths;
    }