diff --git CHANGELOG.txt CHANGELOG.txt
index 87e7d1a..2c9da6b 100644
--- CHANGELOG.txt
+++ CHANGELOG.txt
@@ -140,6 +140,14 @@ Drupal 7.0, xxxx-xx-xx (development version)
 - Added RDF support:
     * Modules can declare RDF namespaces which are serialized in the <html> tag
       for RDFa support.
+- Search engine optimization and web linking:
+     * Added a rel="canonical" link on node and comment pages to prevent
+       duplicate content indexing by search engines.
+     * Added default a rel="shortlink" link that advertises a short link as an
+       alternative to third-party services.
+     * drupal_set_html_head now stores structured data for link, meta, and
+       and other elements, allowing it to be altered by modules before
+       rendering.
 - Field API:
     * Custom data fields may be attached to nodes, users, comments and taxonomy
       terms.
diff --git includes/batch.inc includes/batch.inc
index 289626e..499aeff 100644
--- includes/batch.inc
+++ includes/batch.inc
@@ -190,7 +190,14 @@ function _batch_progress_page_nojs() {
   }
 
   $url = url($batch['url'], array('query' => array('id' => $batch['id'], 'op' => $new_op)));
-  drupal_add_html_head('<meta http-equiv="Refresh" content="0; URL=' . $url . '">');
+  drupal_add_html_head(array(
+    '#type' => 'head_element',
+    '#value' => 'meta',
+    '#attributes' => array(
+      'http-equiv' => 'Refresh',
+      'content' => '0; URL=' . $url,
+    ),
+  ));
 
   return theme('progress_bar', $percentage, $message);
 }
diff --git includes/common.inc includes/common.inc
index 063174e..7cf7d89 100644
--- includes/common.inc
+++ includes/common.inc
@@ -250,12 +250,24 @@ function drupal_get_rdf_namespaces() {
  * Add output to the head tag of the HTML page.
  *
  * This function can be called as long the headers aren't sent.
+ *
+ * @param $data
+ *   Optional renderable array, of type 'head_element' or 'head_title'.
+ * @param $key
+ *   Optional key for identifying the element in hook_html_head_alter().
+ *
+ * @return
+ *   An array of all the store head elements.
  */
-function drupal_add_html_head($data = NULL) {
-  $stored_head = &drupal_static(__FUNCTION__, '');
+function drupal_add_html_head($data = NULL, $key = NULL) {
+  $stored_head = &drupal_static(__FUNCTION__, array());
 
-  if (!is_null($data)) {
-    $stored_head .= $data . "\n";
+  if (isset($data)) {
+    if (isset($key)) {
+      $stored_head[$key] = $data;
+    } else {
+      $stored_head[] = $data;
+    }
   }
   return $stored_head;
 }
@@ -264,8 +276,22 @@ function drupal_add_html_head($data = NULL) {
  * Retrieve output to be displayed in the head tag of the HTML page.
  */
 function drupal_get_html_head() {
-  $output = "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n";
-  return $output . drupal_add_html_head();
+  $head_elements = drupal_add_html_head();
+
+  $meta_element = array(
+    '#type' => 'head_element',
+    '#value' => 'meta',
+    '#attributes' => array(
+      'http-equiv' => 'Content-Type',
+      'content' => 'text/html; charset=utf-8',
+    ),
+  );
+  array_unshift($head_elements, $meta_element);
+
+  drupal_alter('html_head', $head_elements);
+
+  // Return structured data for later rendering.
+  return drupal_render($head_elements);
 }
 
 /**
@@ -2503,9 +2529,44 @@ function base_path() {
  * Add a <link> tag to the page's HEAD.
  *
  * This function can be called as long the HTML header hasn't been sent.
+ * 
+ * @param $attributes
+ *   Associative array of element attributes.
  */
-function drupal_add_link($attributes) {
-  drupal_add_html_head('<link' . drupal_attributes($attributes) . " />\n");
+function drupal_add_link($attributes, $header = FALSE) {
+  $head_element = array(
+	'#type' => 'head_element',
+    '#value' => 'link',
+	'#attributes' => $attributes,
+  );
+
+  if ($header) {
+    $head_element['#attached']['drupal_set_link_header'][] = array($attributes);
+  }
+
+  // Add LINK element under HTML HEAD element
+  drupal_add_html_head($head_element);
+}
+
+/**
+ * Add a HTTP Link: header.
+ * 
+ * @param $attributes
+ *   Associative array of element attributes.
+ */
+function drupal_set_link_header($attributes) {
+  // From drupal_attributes function
+  foreach ($attributes as $attribute => &$data) {
+    if ($attribute != 'href') {
+      if (is_array($data)) {
+        $data = implode(' ', $data);
+      }
+      $data = $attribute . '="' . check_plain($data) . '"';
+    }
+  }
+  $href = '<' . $attributes['href'] . '> ';
+  unset($attributes['href']);
+  drupal_set_header('Link',  $href . implode('; ', $attributes));
 }
 
 /**
diff --git includes/theme.inc includes/theme.inc
index 9c646a0..8a8e94d 100644
--- includes/theme.inc
+++ includes/theme.inc
@@ -2040,7 +2040,11 @@ function template_preprocess_page(&$variables) {
   if (theme_get_setting('toggle_favicon')) {
     $favicon = theme_get_setting('favicon');
     $type = theme_get_setting('favicon_mimetype');
-    drupal_add_html_head('<link rel="shortcut icon" href="' . check_url($favicon) . '" type="' . check_plain($type) . '" />');
+    drupal_add_link(array(
+      'rel' => 'shortcut icon',
+      'href' => check_url($favicon),
+      'type' => $type,
+    ));
   }
 
   // Set up layout variable.
@@ -2214,7 +2218,11 @@ function template_preprocess_maintenance_page(&$variables) {
   if (theme_get_setting('toggle_favicon')) {
     $favicon = theme_get_setting('favicon');
     $type = theme_get_setting('favicon_mimetype');
-    drupal_add_html_head('<link rel="shortcut icon" href="' . check_url($favicon) . '" type="' . check_plain($type) . '" />');
+    drupal_add_link(array(
+      'rel' => 'shortcut icon',
+      'href' => check_url($favicon),
+      'type' => $type,
+    ));
   }
 
   global $theme;
diff --git modules/comment/comment.module modules/comment/comment.module
index f048a8b..ae33b30 100644
--- modules/comment/comment.module
+++ modules/comment/comment.module
@@ -349,9 +349,6 @@ function comment_permalink($comment) {
     $_GET['q'] = 'node/' . $node->nid;
     $_GET['page'] = $page;
 
-    // Set the node path as the canonical URL to prevent duplicate content.
-    drupal_add_link(array('rel' => 'canonical', 'href' => url('node/' . $node->nid)));
-
     // Return the node view, this will show the correct comment in context.
     return menu_execute_active_handler('node/' . $node->nid);
   }
diff --git modules/node/node.module modules/node/node.module
index 0ae1104..5dd5104 100644
--- modules/node/node.module
+++ modules/node/node.module
@@ -1955,6 +1955,10 @@ function node_page_default() {
  */
 function node_page_view($node) {
   drupal_set_title($node->title);
+
+  // Set the node path as the canonical URL to prevent duplicate content.
+  drupal_add_link(array('rel' => 'canonical', 'href' => url('node/' . $node->nid)), TRUE);
+  drupal_add_link(array('rel' => 'shortlink', 'href' => url('node/' . $node->nid, array('alias' => TRUE))), TRUE);
   return node_show($node);
 }
 
diff --git modules/openid/tests/openid_test.module modules/openid/tests/openid_test.module
index b101b50..9a424c8 100644
--- modules/openid/tests/openid_test.module
+++ modules/openid/tests/openid_test.module
@@ -97,7 +97,14 @@ function openid_test_yadis_x_xrds_location() {
  * Menu callback; regular HTML page with <meta> element.
  */
 function openid_test_yadis_http_equiv() {
-  drupal_add_html_head('<meta http-equiv="X-XRDS-Location" content="' . url('openid-test/yadis/xrds', array('absolute' => TRUE)) . '" />');
+  drupal_add_html_head(array(
+    '#type' => 'head_element',
+    '#value' => 'meta',
+    '#attributes' => array(
+      'http-equiv' => 'X-XRDS-Location',
+      'content' => url('openid-test/yadis/xrds', array('absolute' => TRUE)),
+    ),
+  ));
   return t('This page includes a &lt;meta equiv=...&gt; element containing the URL of an XRDS document.');
 }
 
@@ -105,7 +112,10 @@ function openid_test_yadis_http_equiv() {
  * Menu callback; regular HTML page with OpenID 1.0 <link> element.
  */
 function openid_test_html_openid1() {
-  drupal_add_html_head('<link rel="openid.server" href="' . url('openid-test/endpoint', array('absolute' => TRUE)) . '" />');
+  drupal_add_link(array(
+    'rel' => 'openid.server',
+    'href' => url('openid-test/endpoint', array('absolute' => TRUE)),
+  ));
   return t('This page includes a &lt;link rel=...&gt; element containing the URL of an OpenID Provider Endpoint.');
 }
 
@@ -113,7 +123,10 @@ function openid_test_html_openid1() {
  * Menu callback; regular HTML page with OpenID 2.0 <link> element.
  */
 function openid_test_html_openid2() {
-  drupal_add_html_head('<link rel="openid2.provider" href="' . url('openid-test/endpoint', array('absolute' => TRUE)) . '" />');
+  drupal_add_link(array(
+    'rel' => 'openid2.provider',
+    'href' => url('openid-test/endpoint', array('absolute' => TRUE)),
+  ));
   return t('This page includes a &lt;link rel=...&gt; element containing the URL of an OpenID Provider Endpoint.');
 }
 
diff --git modules/simpletest/tests/browser_test.module modules/simpletest/tests/browser_test.module
index ea2ea8f..5845472 100644
--- modules/simpletest/tests/browser_test.module
+++ modules/simpletest/tests/browser_test.module
@@ -61,7 +61,14 @@ function browser_test_print_post_form_submit($form, &$form_state) {
 function browser_test_refresh_meta() {
   if (!isset($_GET['refresh'])) {
     $url = url('browser_test/refresh/meta', array('absolute' => TRUE, 'query' => 'refresh=true'));
-    drupal_add_html_head('<meta http-equiv="Refresh" content="0; URL=' . $url . '">');
+    drupal_add_html_head(array(
+      '#type' => 'head_element',
+      '#value' => 'meta',
+      '#attributes' => array(
+        'http-equiv' => 'Refresh',
+        'content' => '0; URL=' . $url,
+      )
+    ));
     return '';
   }
   echo 'Refresh successful';
diff --git modules/system/system.module modules/system/system.module
index 3eb3656..26087dd 100644
--- modules/system/system.module
+++ modules/system/system.module
@@ -194,6 +194,9 @@ function system_theme() {
     'system_powered_by' => array(
       'arguments' => array('image_path' => NULL),
     ),
+    'head_element' => array(
+      'arguments' => array('element' => NULL),
+    ),
     'meta_generator_html' => array(
       'arguments' => array('version' => NULL),
     ),
@@ -486,6 +489,10 @@ function system_elements() {
     '#theme' => array('hidden'),
   );
 
+  $type['head_element'] = array(
+    '#theme' => 'head_element',
+  );
+
   return $type;
 }
 
@@ -3022,6 +3029,14 @@ function theme_system_compact_link() {
   return $output;
 }
 
+/**
+ * Send Drupal and the major version number in the HTTP headers.
+ *
+ * @ingroup themeable
+ */
+function theme_head_element(array $element) {
+  return '<' . $element['#value'] . drupal_attributes($element['#attributes']) ." />\n";
+}
 
 /**
  * Send Drupal and the major version number in the META GENERATOR HTML.
@@ -3029,7 +3044,14 @@ function theme_system_compact_link() {
  * @ingroup themeable
  */
 function theme_meta_generator_html($version = VERSION) {
-  drupal_add_html_head('<meta name="Generator" content="Drupal ' . $version . ' (http://drupal.org)" />');
+  drupal_add_html_head(array(
+    '#type' => 'head_element',
+    '#value' => 'meta',
+    '#attributes' => array(
+      'name' => 'Generator',
+      'content' => 'Drupal ' . $version . ' (http://drupal.org)',
+    ),
+  ));
 }
 
 /**
