Index: wp-includes/functions.wp-scripts.php
===================================================================
--- wp-includes/functions.wp-scripts.php	(revision 22265)
+++ wp-includes/functions.wp-scripts.php	(working copy)
@@ -183,3 +183,15 @@
 
 	return (bool) $wp_scripts->query( $handle, $list );
 }
+
+function wp_script_add_data( $handle, $key, $value ){
+	global $wp_scripts;
+	if ( ! is_a( $wp_scripts, 'WP_Scripts' ) ) {
+		if ( ! did_action( 'init' ) )
+			_doing_it_wrong( __FUNCTION__, sprintf( __( 'Scripts and styles should not be registered or enqueued until the %1$s, %2$s, or %3$s hooks.' ),
+				'<code>wp_enqueue_scripts</code>', '<code>admin_enqueue_scripts</code>', '<code>init</code>' ), '3.5' );
+		$wp_scripts = new WP_Scripts();
+	}
+
+	return (bool) $wp_scripts->add_data( $handle, $key, $value );
+}
Index: wp-includes/functions.wp-styles.php
===================================================================
--- wp-includes/functions.wp-styles.php	(revision 22265)
+++ wp-includes/functions.wp-styles.php	(working copy)
@@ -190,3 +190,15 @@
 
 	return (bool) $wp_styles->query( $handle, $list );
 }
+
+function wp_style_add_data( $handle, $key, $value ){
+	global $wp_styles;
+	if ( ! is_a( $wp_styles, 'WP_Styles' ) ) {
+		if ( ! did_action( 'init' ) )
+			_doing_it_wrong( __FUNCTION__, sprintf( __( 'Scripts and styles should not be registered or enqueued until the %1$s, %2$s, or %3$s hooks.' ),
+				'<code>wp_enqueue_scripts</code>', '<code>admin_enqueue_scripts</code>', '<code>init</code>' ), '3.5' );
+		$wp_styles = new WP_Styles();
+	}
+
+	return (bool) $wp_styles->add_data( $handle, $key, $value );
+}
Index: wp-includes/class.wp-scripts.php
===================================================================
--- wp-includes/class.wp-scripts.php	(revision 22265)
+++ wp-includes/class.wp-scripts.php	(working copy)
@@ -83,22 +83,24 @@
 			return false;
 		}
 
+		$obj = $this->registered[$handle];
+
 		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 )
+		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;
 
 		if ( $this->do_concat ) {
 			$srce = apply_filters( 'script_loader_src', $src, $handle );
-			if ( $this->in_default_dir($srce) ) {
+			if ( $this->in_default_dir($srce) && ! isset( $obj->extra['conditional'] ) ) {
 				$this->print_code .= $this->print_extra_script( $handle, false );
 				$this->concat .= "$handle,";
 				$this->concat_version .= "$handle$ver";
@@ -119,10 +121,16 @@
 
 		$src = esc_url( apply_filters( 'script_loader_src', $src, $handle ) );
 
+		$cond_before = $cond_after = null;
+		if ( isset($obj->extra['conditional']) && $obj->extra['conditional'] ) {
+			$cond_before = "<!--[if {$obj->extra['conditional']}]>\n";
+			$cond_after = "<![endif]-->\n";
+		}
+
 		if ( $this->do_concat )
-			$this->print_html .= "<script type='text/javascript' src='$src'></script>\n";
+			$this->print_html .= "$cond_before<script type='text/javascript' src='$src'></script>\n$cond_after";
 		else
-			echo "<script type='text/javascript' src='$src'></script>\n";
+			echo "$cond_before<script type='text/javascript' src='$src'></script>\n$cond_after";
 
 		return true;
 	}
Index: wp-content/themes/twentytwelve/header.php
===================================================================
--- wp-content/themes/twentytwelve/header.php	(revision 22265)
+++ 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: wp-content/themes/twentytwelve/functions.php
===================================================================
--- wp-content/themes/twentytwelve/functions.php	(revision 22265)
+++ wp-content/themes/twentytwelve/functions.php	(working copy)
@@ -91,6 +91,12 @@
 	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', true );
+	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).
 	 */
@@ -148,7 +154,7 @@
 	 * 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' );