You can wrap HTML comment tags around the whole section, and individually comment the PHP echo and require statements.
PHP Code:
<!--bof-navigation display-->
<!-- <div id="navMainWrapper">
<div id="navMain">
<ul class="back">
<li><?php //echo '<a href="' . HTTP_SERVER . DIR_WS_CATALOG . '">'; ?><?php //echo HEADER_TITLE_CATALOG; ?></a></li>
<?php if ($_SESSION['customer_id']) { ?>
<li><a href="<?php //echo zen_href_link(FILENAME_LOGOFF, '', 'SSL'); ?>"><?php //echo HEADER_TITLE_LOGOFF; ?></a></li>
<li><a href="<?php //echo zen_href_link(FILENAME_ACCOUNT, '', 'SSL'); ?>"><?php //echo HEADER_TITLE_MY_ACCOUNT; ?></a></li>
<?php
} else {
if (STORE_STATUS == '0') {
?>
<li><a href="<?php //echo zen_href_link(FILENAME_LOGIN, '', 'SSL'); ?>"><?php //echo HEADER_TITLE_LOGIN; ?></a></li>
<?php } } ?>
<?php if ($_SESSION['cart']->count_contents() != 0) { ?>
<li><a href="<?php //echo zen_href_link(FILENAME_SHOPPING_CART, '', 'NONSSL'); ?>"><?php //echo HEADER_TITLE_CART_CONTENTS; ?></a></li>
<li><a href="<?php //echo zen_href_link(FILENAME_CHECKOUT_SHIPPING, '', 'SSL'); ?>"><?php //echo HEADER_TITLE_CHECKOUT; ?></a></li>
<?php }?>
</ul>
</div>
<div id="navMainSearch"><?php //require(DIR_WS_MODULES . 'sideboxes/search_header.php'); ?></div>
<br class="clearBoth" />
</div> -->
<!--eof-navigation display-->