Index: src/wp-content/themes/twentytwelve/functions.php
===================================================================
--- src/wp-content/themes/twentytwelve/functions.php	(revision 30985)
+++ src/wp-content/themes/twentytwelve/functions.php	(working copy)
@@ -133,6 +133,12 @@
 	global $wp_styles;
 
 	/*
+	 * Loads HTML5 JavaScript file to add support for HTML5 elements in older IE versions.
+	 */
+	wp_enqueue_script( 'twentytwelve-html5', get_template_directory_uri() . '/js/html5.js', array(), '1.0' );
+	wp_script_add_data( 'twentytwelve-html5', 'conditional', 'lt IE 9' );
+
+	/*
 	 * Adds JavaScript to pages with the comment form to support
 	 * sites with threaded comments (when in use).
 	 */
@@ -151,7 +157,7 @@
 
 	// Loads the Internet Explorer specific stylesheet.
 	wp_enqueue_style( 'twentytwelve-ie', get_template_directory_uri() . '/css/ie.css', array( 'twentytwelve-style' ), '20121010' );
-	$wp_styles->add_data( 'twentytwelve-ie', 'conditional', 'lt IE 9' );
+	wp_style_add_data( 'twentytwelve-ie', 'conditional', 'lt IE 9' );
 }
 add_action( 'wp_enqueue_scripts', 'twentytwelve_scripts_styles' );
 
Index: src/wp-content/themes/twentytwelve/header.php
===================================================================
--- src/wp-content/themes/twentytwelve/header.php	(revision 30985)
+++ src/wp-content/themes/twentytwelve/header.php	(working copy)
@@ -24,10 +24,6 @@
 <title><?php wp_title( '|', true, 'right' ); ?></title>
 <link rel="profile" href="http://gmpg.org/xfn/11" />
 <link rel="pingback" href="<?php bloginfo( 'pingback_url' ); ?>" />
-<?php // Loads HTML5 JavaScript file to add support for HTML5 elements in older IE versions. ?>
-<!--[if lt IE 9]>
-<script src="<?php echo get_template_directory_uri(); ?>/js/html5.js" type="text/javascript"></script>
-<![endif]-->
 <?php wp_head(); ?>
 </head>
 
Index: src/wp-includes/class.wp-scripts.php
===================================================================
--- src/wp-includes/class.wp-scripts.php	(revision 30985)
+++ src/wp-includes/class.wp-scripts.php	(working copy)
@@ -95,16 +95,25 @@
 		if ( false === $group && in_array($handle, $this->in_footer, true) )
 			$this->in_footer = array_diff( $this->in_footer, (array) $handle );
 
-		if ( null === $this->registered[$handle]->ver )
+		$obj = $this->registered[$handle];
+
+		if ( null === $obj->ver )
 			$ver = '';
 		else
-			$ver = $this->registered[$handle]->ver ? $this->registered[$handle]->ver : $this->default_version;
+			$ver = $obj->ver ? $obj->ver : $this->default_version;
 
 		if ( isset($this->args[$handle]) )
 			$ver = $ver ? $ver . '&amp;' . $this->args[$handle] : $this->args[$handle];
 
-		$src = $this->registered[$handle]->src;
+		$src = $obj->src;
+		$cond_before = $cond_after = '';
+		$conditional = isset( $obj->extra['conditional'] ) ? $obj->extra['conditional'] : '';
 
+		if ( $conditional ) {
+			$cond_before = "<!--[if {$conditional}]>\n";
+			$cond_after = "\n<![endif]-->";
+		}
+
 		if ( $this->do_concat ) {
 			/**
 			 * Filter the script loader source.
@@ -115,7 +124,7 @@
 			 * @param string $handle Script handle.
 			 */
 			$srce = apply_filters( 'script_loader_src', $src, $handle );
-			if ( $this->in_default_dir($srce) ) {
+			if ( $this->in_default_dir( $srce ) && ! $conditional ) {
 				$this->print_code .= $this->print_extra_script( $handle, false );
 				$this->concat .= "$handle,";
 				$this->concat_version .= "$handle$ver";
@@ -140,7 +149,7 @@
 		if ( ! $src )
 			return true;
 
-		$tag = "<script type='text/javascript' src='$src'></script>\n";
+		$tag = "{$cond_before}<script type='text/javascript' src='$src'></script>{$cond_after}\n";
 
 		/** 
 		 * Filter the HTML script tag of an enqueued script.
Index: src/wp-includes/functions.wp-scripts.php
===================================================================
--- src/wp-includes/functions.wp-scripts.php	(revision 30985)
+++ src/wp-includes/functions.wp-scripts.php	(working copy)
@@ -258,3 +258,26 @@
 
 	return (bool) $wp_scripts->query( $handle, $list );
 }
+
+
+/**
+ * Add metadata to a script.
+ *
+ * Works only if the script has already been added.
+ *
+ * Possible values for $key and $value:
+ * 'conditional' string Comments for IE 6, lte IE 7, etc.
+ *
+ * @see WP_Dependency::add_data()
+ *
+ * @since 4.2.0
+ *
+ * @param string $handle Name of the script.
+ * @param string $key    Name of data point for which we're storing a value.
+ * @param mixed  $value  String containing the data to be added.
+ * @return bool True on success, false on failure.
+ */
+function wp_script_add_data( $handle, $key, $value ){
+	global $wp_scripts;
+	return $wp_scripts->add_data( $handle, $key, $value );
+}