Hi this is realy common.
Create an view script like : /views/emails/template.phtml
<body>
<?php echo $this->name; ?>
<h1>Welcome</h1>
<?php echo $this->mysite; ?>
</body>
and when creating the email :
// create view object
$html = new Zend_View();
$html->setScriptPath(APPLICATION_PATH . '/modules/default/views/emails/');
// assign valeues
$html->assign('name', 'John Doe');
$html->assign('site', 'limespace.de');
// create mail object
$mail = new Zend_Mail('utf-8');
// render view
$bodyText = $html->render('template.phtml');
// configure base stuff
$mail->addTo('john@doe.com');
$mail->setSubject('Welcome to Limespace.de');
$mail->setFrom('support@limespace.de','Limespace');
$mail->setBodyHtml($bodyText);
$mail->send();