Simple and quick way to make links for a domain nofollow in your posts & pages content if, like for me, all of the nofollow plugins failed at the task or broke your site.

nofollow.php

<?php
  /**
   * Allows you to create nofollow links easily in WP content for specific urls and
   *
   * File:    nofollow.php
   * User:    marvinroman
   * Created: 6/14/13
   *
   * Change the items in [] as well as the subdomain array
   * If you don't know the subdomains run the file once with the array empty and it will show you all the found subdomains without making any changes
   * Place this file in your root WP and then visit http://wpdomain.com/nofollow.php
   * Probably best to chmod 000 and run from terminal like /usr/local/bin/php ./nofollow.php 
   */

  // url to mark nofollow
  $url        = "[nofollowdomain.com]";

  // list of subdomains of url above to mark nofollow
  $subDomains = array(
    'www',
    'forum',
    'information',
    'faq',
    'resources',
    ''
  ); // best to include '' as well for base domain

  // sites base url
  $self       = "[blog.domain.com]";
  $disableRootSelf   = true;// whether to also ban link to root self ie http://www.self.com/


  include_once('wp-config.php'); //needs to be in root so it has access to wp-config where DB info is held

  $link = mysql_connect(DB_HOST, DB_USER, DB_PASSWORD);

  $findSQL = "SELECT `ID`, `post_content` FROM `" . DB_NAME . "`.`wp_posts` WHERE `post_content` LIKE '%$url%' AND `post_type` NOT LIKE 'revision';";

  $result = mysql_query($findSQL, $link);

  $foundSubDomains = array();
  $ids             = array();
  while ($row = mysql_fetch_array($result)) {


    $content = $row[1];
    if ($disableRootSelf && strpos($content, $self) > 0):
      $escapedURL = str_replace(array('/', '.'), array('\/', '\.'), $self);
      $preREGEX   = '';
      $postREGEX  = '\/?';
      $findREGEX  = '/<a\s+(t[a-z]+="[^"]+")?\s+href="http:\/\/(' . $preREGEX . $escapedURL . ')(' . $postREGEX . ')"/';
      $content    = preg_replace($findREGEX, '<a rel="nofollow" href="http://$2" $1', $content);
    endif;

    $escapedURL = str_replace(array('/', '.'), array('\/', '\.'), $url);
    $preREGEX   = sprintf('(%s)\.?', implode('|', $subDomains));
    $postREGEX  = '[^"]*';
    $findREGEX  = '/<a[\s]+(t[a-z]+="[^"]+")?[\s]*href="http:\/\/(' . $preREGEX . $escapedURL . ')(' . $postREGEX . ')"/';
    $content    = preg_replace($findREGEX, '<a rel="nofollow" href="http://$2" $1', $content);

    $findSQL = '/href="http:\/\/([a-z]+)\.' . $escapedURL . '/';
    if (preg_match_all($findSQL, $content, $matches) >= 1) {
      foreach ($matches[1] as $sub) {
        array_push($foundSubDomains, $sub);
      }
      $foundSubDomains = array_unique($foundSubDomains);
    }

    if (!is_null($content)) {

      $replaced = mysql_real_escape_string($content, $link);
      $replaceSQL = "UPDATE `" . DB_NAME . "`.`wp_posts` SET `post_content` = '" . $content . "' WHERE `ID` = '" . $row[0] . "';";

      if (count($subDomains) > 0) mysql_query($replaceSQL, $link);
      array_push($ids, $row[0]);
    }
  }
  echo "\nList of No Follow Subdomains for $url\n";
  echo implode(",\n", $subDomains);
  echo "\n\nList of Found Subdomains for $url \n";
  echo implode(",\n", $foundSubDomains);
  echo "\n\nPosts affected on $self\n";
  echo count($ids) . "\n";