Index: wp-includes/script-loader.php
===================================================================
--- wp-includes/script-loader.php	(revision 6163)
+++ wp-includes/script-loader.php	(working copy)
@@ -421,4 +421,24 @@
 	}
 	$wp_scripts->enqueue( $handle );
 }
+
+function wp_prototype_before_jquery( $js_array ) {
+	if ( false === $jquery = array_search( 'jquery', $js_array ) )
+		return $js_array;
+
+	if ( false === $prototype = array_search( 'prototype', $js_array ) )
+		return $js_array;
+
+	if ( $prototype < $jquery )
+		return $js_array;
+
+	unset($js_array[$prototype]);
+
+	array_splice( $js_array, $jquery, 0, 'prototype' );
+
+	return $js_array;
+}
+
+add_filter( 'print_scripts_array', 'wp_prototype_before_jquery' );
+
 ?>