One of the most basic SEO checks is to see if the website suffers from canonicalisation problems. A site suffers from this if it can be accessed at both http://domain.com and www.domain.com this is because the search engines see the www as a subdomain and therefore considers the two sites to be duplicates of each other.
Thankfully if your website is on an Apache server it is easy to fix.
Simply add the following code to your .htaccess file in the root directory:
RewriteEngine On
RewriteCond %{HTTP_HOST} ^domain\.com$ [NC]
RewriteRule ^(.*)$ http://www.domain.com/$1 [R=301,L]
Another canonicalisation problem is when you can access both http://www.domain.com and http://www.domain.com/index.php, again the search engines can see these pages as duplicate.
This can also be fixed easily by adding the following rewrite rule to your .htaccess file in the root directory.
RewriteEngine On
RewriteCond %{THE_REQUEST} ^[A-Z]{3,9}\ /index\.php
RewriteRule ^index\.php$ http://www.domain.com/ [R=301,L]