I use Zend_Layout and put the CSS references in the layout.phtml
My layout.phtml looks like this.
Code:
<?php echo $this->doctype(Zend_View_Helper_Doctype::XHTML1_TRANSITIONAL); ?>
<html>
<head>
<?= $this->headMeta(); ?>
<?= $this->headTitle(); ?>
<link type="text/css" rel="stylesheet" media="screen" href="<?= $this->baseUrl() . '/styles/default.css'; ?>">
<link type="text/css" rel="stylesheet" media="screen" href="<?= $this->baseUrl() . '/scripts/jquery.jdMenu.css'; ?>">
<script src="<?= $this->baseUrl() . '/scripts/jquery-1.2.3.js'; ?>" type="text/javascript"></script>
<script src="<?= $this->baseUrl() . '/scripts/jquery.dimensions.js'; ?>" type="text/javascript"></script>...etc
I hope that helps.