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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