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<!-- Might as well keep your header.php clean and insert the shim from the functions.php file. -->

// add ie conditional html5 shim to header
function add_ie_html5_shim () {
    echo '<!--[if lt IE 9]>';
    echo '<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>';
    echo '<![endif]-->';
}
add_action('wp_head', 'add_ie_html5_shim');

<!-- The shim is to enable HTML5 elements to be able to be styled through CSS in Internet Explorer versions less than 9. -->