A you might know, or not know, www.site.com, www.site.com/index.php, site.com and site.com/index.php are 4 different pages for search engines, although you see the same page.

To avoid the problem with duplicate content you have to have: Apache server running and mod_rewrite module installed. Now, somewhere in your .htaccess file include this code:

Options +FollowSymlinks -Indexes
RewriteEngine On

RewriteCond %{HTTP_HOST} ^yourdomain.com$ [NC]
RewriteRule ^(.*)$ http://www.yourdomain.com/$1 [R=301,L]

RewriteCond %{THE_REQUEST} /index\.php\ HTTP/
RewriteRule ^index\.php$ / [R=301,L]

If first two lines already exist in the .htaccess, add the rest of the code bellow without them. Thus .htaccess will forward all 4 index/home pages to www.yourhost.com. You probably can use other extension instead of php, like html, cfm - not sure about it, never tried but my intuition tells me it will work. [b]-Indexes[/b] is optional. It is small bonus. This directive will disallow access to directories without index file in them. This will save you the time to upload blank index.html files in such directories, the content of which you don’t want to be visible to bots and guests.