Install Lynx web browser to test site. In Ubuntu:

% apt-get install lynx-cur
% lynx www.example.com

Install a sitemap following sitemap standards (use a sitemap generator):

<?xml version="1.0" encoding="UTF-8"?>
<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9"
        xmlns:image="http://www.google.com/schemas/sitemap-image/1.1"
        xmlns:video="http://www.google.com/schemas/sitemap-video/1.1">
  <url> 
    <loc>http://www.example.com/foo.html</loc> 
    <image:image>
       <image:loc>http://example.com/image.jpg</image:loc> 
    </image:image>
    <video:video>     
      <video:content_loc>http://www.example.com/video123.flv</video:content_loc>
      <video:player_loc allow_embed="yes"
      autoplay="ap=1">http://www.example.com/videoplayer.swf?video=123</video:player_loc>
      <video:thumbnail_loc>http://www.example.com/thumbs/123.jpg</video:thumbnail_loc>
      <video:title>Grilling steaks for summer</video:title>  
      <video:description>Get perfectly done steaks every time</video:description>
    </video:video>
  </url>
</urlset>

List all files with a certain datetime stamp that match the compromised files:

% ls -l -R | grep --color=auto '2011-08-02 16:18'

List all files with a certain string inside:

% grep -H -r "redeem reward" /home/tom | less

Update server operating system. Eg. Ubuntu:

% apt-get update
% apt-get upgrade

Upgrade operating system to newer version. Eg. Ubuntu:

% do-release-upgrade

Base64decode for encrypted malware

PHP Decoder: Decrypting malware

Cleaning Eval-base64-decode PHP virus

Creating Sitemaps

Google: Webmaster Guidelines

Google: Cleaning Your Site

Google: Hacked Content

Hakipedia: Local File Inclusion

Imperva: Remote and Local File Inclusion Vulnerabilities (PDF)

Sucuri: Website Attack Cleaning

Sucuri: Website Malware Scanner