If you have pages such as index.php, or index.htm on your site and people link to these sites then you will hav duplicate content listed by search engines via www.domain.com and www.domain.com/index.htm etc.
The way to get around this is by using mod_rewrite.
RewriteCond %{THE_REQUEST} ^GET .*/index.(php|html) HTTP
RewriteRule ^(.*)index.(php|html)$ /$1 [R=301,L]
After entering this into your .htacess file all links that point to www.domain.com/index.php will take you to www.domain.com
Redirect default pages to the domain root