Index: wp-includes/formatting.php
===================================================================
--- wp-includes/formatting.php	(revision 16834)
+++ wp-includes/formatting.php	(working copy)
@@ -1312,12 +1312,19 @@
  */
 function _make_url_clickable_cb($matches) {
 	$url = $matches[2];
+	$suffix = '';
+	
+	/** Include parentheses in the URL only if paired **/
+	while ( substr_count( $url, '(' ) < substr_count( $url, ')' ) ) {
+		$suffix = strrchr( $url, ')' ) . $suffix; 
+		$url = substr( $url, 0, strrpos( $url, ')' ) ); 
+	}
 
 	$url = esc_url($url);
 	if ( empty($url) )
 		return $matches[0];
 
-	return $matches[1] . "<a href=\"$url\" rel=\"nofollow\">$url</a>";
+	return $matches[1] . "<a href=\"$url\" rel=\"nofollow\">$url</a>" . $suffix;
 }
 
 /**
@@ -1379,7 +1386,7 @@
 function make_clickable($ret) {
 	$ret = ' ' . $ret;
 	// in testing, using arrays here was found to be faster
-	$ret = preg_replace_callback('#(?<=[\s>])(\()?([\w]+?://(?:[\w\\x80-\\xff\#$%&~/=?@\[\](!+-]|[.,;:](?![\s<]|(\))?([\s]|$))|(?(1)\)(?![\s<.,;:]|$)|\)))+)#is', '_make_url_clickable_cb', $ret);
+	$ret = preg_replace_callback('#(?<!=[\'"])(?<=[*\')+.,;:!&$\s>])(\()?([\w]+?://(?:[\w\\x80-\\xff\#%~/?@\[\]-]|[\'*(+.,;:!=&$](?![\b\)]|(\))?([\s]|$))|(?(1)\)(?![\s<.,;:]|$)|\)))+)#is', '_make_url_clickable_cb', $ret);
 	$ret = preg_replace_callback('#([\s>])((www|ftp)\.[\w\\x80-\\xff\#$%&~/.\-;:=,?@\[\]+]+)#is', '_make_web_ftp_clickable_cb', $ret);
 	$ret = preg_replace_callback('#([\s>])([.0-9a-z_+-]+)@(([0-9a-z-]+\.)+[0-9a-z]{2,})#i', '_make_email_clickable_cb', $ret);
 	// this one is not in an array because we need it to run last, for cleanup of accidental links within links