diff --git CHANGELOG.txt CHANGELOG.txt
index 87e7d1a..35a5eae 100644
--- CHANGELOG.txt
+++ CHANGELOG.txt
@@ -140,6 +140,13 @@ 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 on node and comment pages
+       that advertises a short link as an alternative to third-party services.
+     * drupal_set_html_head now stores structured data for link, meta, 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..7cd4b80 100644
--- includes/batch.inc
+++ includes/batch.inc
@@ -190,7 +190,7 @@ 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('batch_meta_refresh', array('#markup' => '<meta http-equiv="Refresh" content="0; URL=' . $url . '">'));
 
   return theme('progress_bar', $percentage, $message);
 }
diff --git includes/common.inc includes/common.inc
index 063174e..1a27343 100644
--- includes/common.inc
+++ includes/common.inc
@@ -250,12 +250,21 @@ 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 $key
+ *   Key for identifying the element in hook_html_head_alter(). Required if
+ *   $data is not NULL.
+ * @param $data
+ *   Optional renderable array.
+ *
+ * @return
+ *   An array of all the stored head elements.
  */
-function drupal_add_html_head($data = NULL) {
-  $stored_head = &drupal_static(__FUNCTION__, '');
+function drupal_add_html_head($key = NULL, $data = NULL) {
+  $stored_head = &drupal_static(__FUNCTION__, array());
 
-  if (!is_null($data)) {
-    $stored_head .= $data . "\n";
+  if (isset($data) && isset($key)) {
+    $stored_head[$key] = $data;
   }
   return $stored_head;
 }
@@ -264,8 +273,29 @@ function drupal_add_html_head($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();
+  $head_elements = drupal_add_html_head();
+  // Get the major version.
+  list($version, ) = explode('.', VERSION);
+  // Add default elements. Make sure the Content-Type comes first.
+  $meta_elements['system_meta_content_type'] = array(
+    '#markup' => '<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />',
+  );
+  // Send Drupal and the major version number in the META GENERATOR HTML.
+  $meta_elements['system_meta_generator'] = array(
+    '#markup' => '<meta name="Generator" content="Drupal ' . $version . ' (http://drupal.org)" />',
+  );
+  // Send Drupal and the major version number in the HTTP headers.
+  $meta_elements['system_meta_generator']['#attached']['drupal_set_header'][] = array('X-Generator', 'Drupal ' . $version . ' (http://drupal.org)');
+  // Make sure the Content-Type comes first.
+  $head_elements = array_merge($meta_elements, $head_elements);
+  // Add a CR to each element for nicer printing.
+  foreach ($head_elements as $key => $element) {
+    if (!isset($element['#suffix'])) {
+      $head_elements[$key]['#suffix'] = "\n";
+    }
+  }
+  drupal_alter('html_head', $head_elements);
+  return drupal_render($head_elements);
 }
 
 /**
@@ -290,11 +320,13 @@ function drupal_add_feed($url = NULL, $title = '') {
 
   if (!is_null($url) && !isset($stored_feed_links[$url])) {
     $stored_feed_links[$url] = theme('feed_icon', $url, $title);
-
-    drupal_add_link(array('rel' => 'alternate',
-                          'type' => 'application/rss+xml',
-                          'title' => $title,
-                          'href' => $url));
+    $attributes = array(
+      'rel' => 'alternate',
+      'type' => 'application/rss+xml',
+      'title' => $title,
+      'href' => $url,
+    );
+    drupal_add_link('system_feed_' . $url, $attributes);
   }
   return $stored_feed_links;
 }
@@ -2300,10 +2332,13 @@ function url($path = NULL, array $options = array()) {
  *
  * @param $attributes
  *   An associative array of HTML attributes.
+ * @param $separator
+ *   Optional string for separating attributes. Defaults to a space.
+ *
  * @return
  *   An HTML string ready for insertion in a tag.
  */
-function drupal_attributes(array $attributes = array()) {
+function drupal_attributes(array $attributes = array(), $separator = ' ') {
   foreach ($attributes as $attribute => &$data) {
     if (is_array($data)) {
       $data = implode(' ', $data);
@@ -2500,12 +2535,29 @@ function base_path() {
 }
 
 /**
- * Add a <link> tag to the page's HEAD.
+ * Add a LINK tag to the page's HEAD.
  *
  * This function can be called as long the HTML header hasn't been sent.
+ * 
+ * @param $key
+ *   A unique string key for identifying this link.
+ * @param $attributes
+ *   Associative array of element attributes.
+ * @param $header
+ *   Optional flag to determine if a HTTP Link: header should be sent.
  */
-function drupal_add_link($attributes) {
-  drupal_add_html_head('<link' . drupal_attributes($attributes) . " />\n");
+function drupal_add_link($key, $attributes, $header = FALSE) {
+  $head_element = array(
+    '#markup' => '<link' . drupal_attributes($attributes) . ' />',
+  );
+
+  if ($header) {
+    // Set a HTTP Link: header also.
+    $href = '<' . check_plain($attributes['href']) . '>';
+    unset($attributes['href']);
+    $head_element['#attached']['drupal_set_header'][] = array('Link',  $href . drupal_attributes($attributes, '; '), TRUE);
+  }
+  drupal_add_html_head($key, $head_element);
 }
 
 /**
diff --git includes/theme.inc includes/theme.inc
index 1c5a80f..701245a 100644
--- includes/theme.inc
+++ includes/theme.inc
@@ -2093,7 +2093,7 @@ 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($type) . '" />');
+    drupal_add_html_head('favicon_link', array('#markup' => '<link rel="shortcut icon" href="' . check_url($favicon) . '" type="' . check_plain($type) . '" />'));
   }
 
   // Set up layout variable.
@@ -2267,7 +2267,7 @@ 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($type) . '" />');
+    drupal_add_html_head('favicon_link', array('#markup' => '<link rel="shortcut icon" href="' . check_url($favicon) . '" type="' . check_plain($type) . '" />'));
   }
 
   global $theme;
diff --git modules/book/book.module modules/book/book.module
index 9f2fabe..75bdc39 100644
--- modules/book/book.module
+++ modules/book/book.module
@@ -914,21 +914,21 @@ function template_preprocess_book_navigation(&$variables) {
 
     if ($prev = book_prev($book_link)) {
       $prev_href = url($prev['href']);
-      drupal_add_link(array('rel' => 'prev', 'href' => $prev_href));
+      drupal_add_link('book_prev_link', array('rel' => 'prev', 'href' => $prev_href));
       $variables['prev_url'] = $prev_href;
       $variables['prev_title'] = check_plain($prev['title']);
     }
 
     if ($book_link['plid'] && $parent = book_link_load($book_link['plid'])) {
       $parent_href = url($parent['href']);
-      drupal_add_link(array('rel' => 'up', 'href' => $parent_href));
+      drupal_add_link('book_up_link', array('rel' => 'up', 'href' => $parent_href));
       $variables['parent_url'] = $parent_href;
       $variables['parent_title'] = check_plain($parent['title']);
     }
 
     if ($next = book_next($book_link)) {
       $next_href = url($next['href']);
-      drupal_add_link(array('rel' => 'next', 'href' => $next_href));
+      drupal_add_link('book_next_link', array('rel' => 'next', 'href' => $next_href));
       $variables['next_url'] = $next_href;
       $variables['next_title'] = check_plain($next['title']);
     }
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/' . $node->nid);
   }
diff --git modules/node/node.module modules/node/node.module
index 0ae1104..5bdbcf4 100644
--- modules/node/node.module
+++ modules/node/node.module
@@ -1955,6 +1955,10 @@ function node_page_default() {
  */
 function node_page_view($node) {
   drupal_set_title($node->title);
+  // Set the node path as the canonical URL to prevent duplicate indexing.
+  drupal_add_link('node_canonical_link', array('rel' => 'canonical', 'href' => url('node/' . $node->nid)), TRUE);
+  // Set the non-aliased path as a default shortlink.
+  drupal_add_link('node_shortlink_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..7b8a6cf 100644
--- modules/openid/tests/openid_test.module
+++ modules/openid/tests/openid_test.module
@@ -97,7 +97,8 @@ 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)) . '" />');
+  $url = url('openid-test/yadis/xrds', array('absolute' => TRUE));
+  drupal_add_html_head('openid_test_yadis_xrds', array('#markup' => '<meta http-equiv="X-XRDS-Location" content="' . $url . '" />'));
   return t('This page includes a &lt;meta equiv=...&gt; element containing the URL of an XRDS document.');
 }
 
@@ -105,7 +106,11 @@ 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)) . '" />');
+  $attributes = array(
+    'rel' => 'openid.server',
+    'href' => url('openid-test/endpoint', array('absolute' => TRUE)),
+  );
+  drupal_add_link('openid_test_html_openid1', $attributes);
   return t('This page includes a &lt;link rel=...&gt; element containing the URL of an OpenID Provider Endpoint.');
 }
 
@@ -113,7 +118,11 @@ 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)) . '" />');
+  $attributes = array(
+    'rel' => 'openid2.provider',
+    'href' => url('openid-test/endpoint', array('absolute' => TRUE)),
+  );
+  drupal_add_link('openid_test_html_openid2', $attributes);
   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..2fdf7ab 100644
--- modules/simpletest/tests/browser_test.module
+++ modules/simpletest/tests/browser_test.module
@@ -61,7 +61,7 @@ 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('browser_test_meta_refresh', array('#markup' => '<meta http-equiv="Refresh" content="0; URL=' . $url . '">'));
     return '';
   }
   echo 'Refresh successful';
diff --git modules/system/system.api.php modules/system/system.api.php
index df2ff32..995844d 100644
--- modules/system/system.api.php
+++ modules/system/system.api.php
@@ -2213,6 +2213,27 @@ function hook_drupal_goto_alter(array $args) {
 }
 
 /**
+ * Alter XHTML HEAD tags before they are rendered by drupal_get_html_head().
+ *
+ * Elements available to be altered are only those added using drupal_add_link()
+ * or drupal_add_html_head(). CSS and JS files are handled using
+ * drupal_add_css() and drupal_add_js(), so the head links for those files will
+ * not appear in the $head_elements array.
+ *
+ * @param $head_elements
+ *   An array of renderable elements. Typically they will have a #markup
+ *   key, but might have a #type if they are not simple markup.
+ */
+function hook_html_head_alter(&$head_elements) {
+  foreach($head_elements as $key => $element) {
+    if ($key == 'node_canonical_link') {
+      // I want a custom canonical url.
+      $head_elements[$key]['#markup'] = mymodule_canonical_link();
+    }
+  }
+}
+
+/**
  * Alter MIME type mappings used to determine MIME type from a file extension.
  *
  * This hook is run when file_mimetype_mapping() is called. It is used to
diff --git modules/system/system.module modules/system/system.module
index 3eb3656..2034439 100644
--- modules/system/system.module
+++ modules/system/system.module
@@ -194,12 +194,6 @@ function system_theme() {
     'system_powered_by' => array(
       'arguments' => array('image_path' => NULL),
     ),
-    'meta_generator_html' => array(
-      'arguments' => array('version' => NULL),
-    ),
-    'meta_generator_header' => array(
-      'arguments' => array('version' => NULL),
-    ),
     'system_compact_link' => array(),
     'system_run_cron_image' => array(
       'arguments' => array('image_path' => NULL),
@@ -1496,22 +1490,6 @@ function system_init() {
 }
 
 /**
- * Implement MODULE_preprocess_HOOK().
- */
-function system_preprocess_page(&$variables) {
-  // Get the major version
-  list($version, ) = explode('.', VERSION);
-
-  // Emit the META tag in the HTML HEAD section
-  theme('meta_generator_html', $version);
-
-  // Emit the HTTP Header too
-  theme('meta_generator_header', $version);
-
-  $variables['head'] = drupal_get_html_head();
-}
-
-/**
  * Implement hook_user_form().
  */
 function system_user_form(&$edit, $account, $category) {
@@ -3022,25 +3000,6 @@ function theme_system_compact_link() {
   return $output;
 }
 
-
-/**
- * Send Drupal and the major version number in the META GENERATOR HTML.
- *
- * @ingroup themeable
- */
-function theme_meta_generator_html($version = VERSION) {
-  drupal_add_html_head('<meta name="Generator" content="Drupal ' . $version . ' (http://drupal.org)" />');
-}
-
-/**
- * Send Drupal and the major version number in the HTTP headers.
- *
- * @ingroup themeable
- */
-function theme_meta_generator_header($version = VERSION) {
-  drupal_set_header('X-Generator', 'Drupal ' . $version . ' (http://drupal.org)');
-}
-
 /**
  * Implement hook_image_toolkits().
  */
