Index: themes/bluemarine/page.tpl.php
===================================================================
--- themes/bluemarine/page.tpl.php	(revision 5734)
+++ themes/bluemarine/page.tpl.php	(working copy)
@@ -13,8 +13,11 @@
 <table border="0" cellpadding="0" cellspacing="0" id="header">
   <tr>
     <td id="logo">
-      <?php if ($logo) { ?><a href="./" title="Home"><img src="<?php print $logo ?>" alt="Home" /></a><?php } ?>
-      <?php if ($site_name) { ?><h1 class='site-name'><a href="./" title="Home"><?php print $site_name ?></a></h1><?php } ?>
+
+  <?php if ($logo) { ?><a href="<?php print $base_url_path ?>"
+    title="Home"><img src="<?php print $logo ?>" alt="Home" /></a><?php } ?>
+  <?php if ($site_name) { ?><h1 class='site-name'><a href="<?php print $base_url_path ?>"
+    title="Home"><?php print $site_name ?></a></h1><?php } ?>
       <?php if ($site_slogan) { ?><div class='site-slogan'><?php print $site_slogan ?></div><?php } ?>
     </td>
     <td id="menu">
@@ -41,7 +44,6 @@
         <div class="tabs"><?php print $tabs ?></div>
         <?php print $help ?>
         <?php print $messages ?>
-
         <?php print $content; ?>
       </div>
     </td>
Index: themes/engines/phptemplate/phptemplate.engine
===================================================================
--- themes/engines/phptemplate/phptemplate.engine	(revision 5734)
+++ themes/engines/phptemplate/phptemplate.engine	(working copy)
@@ -140,6 +140,7 @@
  * into a pluggable template engine.
  */
 function phptemplate_page($content) {
+  global $base_url_path;
   /* Set title and breadcrumb to declared values */
 
   if ($_GET['q'] == variable_get('site_frontpage', 'node')) {
@@ -185,6 +186,7 @@
   }
 
   $variables = array(
+    'base_url_path'       => $base_url_path,
     'breadcrumb'          => theme('breadcrumb', drupal_get_breadcrumb()),
     'closure'             => theme('closure'),
     'content'             => '<!-- begin content -->' . $content . '<!-- end content -->',
Index: themes/pushbutton/page.tpl.php
===================================================================
--- themes/pushbutton/page.tpl.php	(revision 5734)
+++ themes/pushbutton/page.tpl.php	(working copy)
@@ -16,7 +16,7 @@
     <td id="home" width="10%">
 
       <?php if ($logo) : ?>
-        <a href="<?php print url() ?>" title="Home"><img src="<?php print($logo) ?>" alt="Home" width="144" height="63" border="0" /></a>
+        <a href="<?php print $base_url_path ?>" title="Home"><img src="<?php print($logo) ?>" alt="Home" width="144" height="63" border="0" /></a>
       <?php endif; ?>
 
     </td>
@@ -24,7 +24,7 @@
     <td id="site-info" width="20%">
 
       <?php if ($site_name) : ?>
-        <div class='site-name'><a href="<?php print url() ?>" title="Home"><?php print($site_name) ?></a></div>
+        <div class='site-name'><a href="<?php print $base_url_path ?>" title="Home"><?php print($site_name) ?></a></div>
       <?php endif;?>
 
       <?php if ($site_slogan) : ?>
Index: includes/bootstrap.inc
===================================================================
--- includes/bootstrap.inc	(revision 5735)
+++ includes/bootstrap.inc	(working copy)
@@ -840,9 +840,11 @@
 
   switch ($phase) {
     case DRUPAL_BOOTSTRAP_DATABASE:
-      global $db_url, $db_prefix, $base_url;
+      global $db_url, $db_prefix, $base_url, $base_url_path;
       $conf = array();
       require_once conf_init() .'/settings.php';
+      $parts = parse_url($base_url);
+      $base_url_path = (isset($parts['path']) ? $parts['path'] . '/' : '/');
       require_once './includes/database.inc';
       // Initialize the default database.
       db_set_active();
Index: includes/common.inc
===================================================================
--- includes/common.inc	(revision 5735)
+++ includes/common.inc	(working copy)
@@ -114,11 +114,10 @@
  * Retrieve output to be displayed in the head tag of the HTML page.
  */
 function drupal_get_html_head() {
-  global $base_url;
+  global $base_url_path;
 
   $output = "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n";
-  $output .= "<base href=\"$base_url/\" />\n";
-  $output .= theme('stylesheet_import', 'misc/drupal.css');
+  $output .= theme('stylesheet_import', $base_url_path .'misc/drupal.css');
 
   return $output . drupal_set_html_head();
 }
@@ -951,7 +950,7 @@
  * alternative than url().
  */
 function url($path = NULL, $query = NULL, $fragment = NULL, $absolute = FALSE) {
-  global $base_url;
+  global $base_url, $base_url_path;
 
   static $script;
 
@@ -968,7 +967,7 @@
     $fragment = '#'. $fragment;
   }
 
-  $base = ($absolute ? $base_url .'/' : '');
+  $base = ($absolute ? $base_url . '/' : $base_url_path);
 
   if (variable_get('clean_url', '0') == '0') {
     if (isset($path)) {
@@ -1174,13 +1173,15 @@
  * depends on the 'killswitch' inside it.
  */
 function drupal_add_js($file) {
+  global $base_url_path;
   static $sent = array();
+
   if (!isset($sent['misc/drupal.js'])) {
-    drupal_set_html_head('<script type="text/javascript" src="misc/drupal.js"></script>');
+    drupal_set_html_head('<script type="text/javascript" src="'. $base_url_path .'misc/drupal.js"></script>');
     $sent['misc/drupal.js'] = true;
   }
   if (!isset($sent[$file])) {
-    drupal_set_html_head('<script type="text/javascript" src="'. check_url($file) .'"></script>');
+    drupal_set_html_head('<script type="text/javascript" src="'. check_url($base_url_path . $file) .'"></script>');
     $sent[$file] = true;
   }
 }
Index: includes/theme.inc
===================================================================
--- includes/theme.inc	(revision 5735)
+++ includes/theme.inc	(working copy)
@@ -263,7 +263,7 @@
  *   The value of the requested setting, NULL if the setting does not exist.
  */
 function theme_get_setting($setting_name, $refresh = FALSE) {
-  global $theme_key;
+  global $theme_key, $base_url_path;
   static $settings;
 
   if (empty($settings) || $refresh) {
@@ -281,11 +281,12 @@
     }
 
     if ($settings['toggle_logo']) {
+      $settings['logo'] = $base_url_path;
       if ($settings['default_logo']) {
-        $settings['logo'] = dirname($theme_object->filename) .'/logo.png';
+        $settings['logo'] .= dirname($theme_object->filename) .'/logo.png';
       }
       elseif ($settings['logo_path']) {
-        $settings['logo'] = $settings['logo_path'];
+        $settings['logo'] .= $settings['logo_path'];
       }
     }
 
@@ -313,10 +314,12 @@
  * drupal_set_html_head() to enforce the correct CSS cascading order.
  */
 function theme_add_style($path = '', $media = 'all') {
+  global $base_url_path;
   static $styles = array();
+
   if ($path) {
     $style = new stdClass();
-    $style->path = $path;
+    $style->path = $base_url_path . $path;
     $style->media = $media;
     $styles[] = $style;
   }
@@ -493,9 +496,11 @@
  *   A string containing the image tag.
  */
 function theme_image($path, $alt = '', $title = '', $attributes = NULL, $getsize = TRUE) {
+  global $base_url_path;
+
   if (!$getsize || (is_file($path) && (list($width, $height, $type, $image_attributes) = @getimagesize($path)))) {
     $attributes = drupal_attributes($attributes);
-    return '<img src="'. check_url($path) .'" alt="'. check_plain($alt) .'" title="'. check_plain($title) .'" '. $image_attributes . $attributes .'/>';
+    return '<img src="'. check_url($base_url_path . $path) .'" alt="'. check_plain($alt) .'" title="'. check_plain($title) .'" '. $image_attributes . $attributes .'/>';
   }
 }