Index: commands/core/core.drush.inc
===================================================================
--- commands/core/core.drush.inc	(revision 39134)
+++ commands/core/core.drush.inc	(working copy)
@@ -47,10 +47,14 @@
     'description' => "Run php script(s).",
     'examples' => array(
       'drush script update_variables.php' => 'Run variables.php script',
+      'drush script variables.php --script_path=/path/to/scripts' => 'Run script from specified path',
     ),
     'arguments' => array(
       'path/to/script' => 'One or more file paths. Paths may be absolute or relative to the current working dir.',
     ),
+    'options' => array(
+      '--script_path' => "Additional paths to search for scripts.  Use POSIX path separator (':').",
+    ),
   );
   $items['cache clear'] = array(
     'description' => 'Clear all caches.'
@@ -295,10 +299,25 @@
  */
 function drush_core_script() {
   $scripts = func_get_args();
+  
+  // Array of paths to search for scripts
+  $searchpath = array();
+  $searchpath[] = drush_cwd();
+  
+  // Additional script paths, specified by 'script_path' option
+  if ($script_path = drush_get_option('script_path', FALSE)) {
+    foreach (explode(":", $script_path) as $path) {
+      $searchpath[] = $path;
+    }
+  }
+  
   foreach ($scripts as $script) {
-    $script_filename = drush_cwd() . '/' . $script;
-    if (file_exists($script_filename)) {
-      include($script_filename);
+    foreach($searchpath as $path) {
+      $script_filename = $path . '/' . $script;
+      if (file_exists($script_filename)) {
+        include($script_filename);
+        break;
+      }
     }
   }
 }
Index: example.drushrc.php
===================================================================
--- example.drushrc.php	(revision 39371)
+++ example.drushrc.php	(working copy)
@@ -37,6 +37,9 @@
 // Enable verbose mode.
 # $options['v'] = 1; 
 
+// Specify additional directories to search for scripts
+// Use POSIX path separator (':')
+# $options['script_path'] = 'sites/all/scripts:profiles/myprofile/scripts';
 
 /*
  * Customize this associative array with your own tables. This is the