One way to do it is using the `wp_head` action:

    function wpse85495_header() {
    ?>
    <!--[if IE]>
      <link rel="stylesheet" href="<?php bloginfo('stylesheet_directory'); ?>/ie.css" type="text/css" />
    <![endif]-->
    <?php
    }
    add_action('wp_head','wpse85495_header');

but I think the prefered way is using `wp_enqueue_style()` in a way described here:

http://core.trac.wordpress.org/ticket/10618#comment:6