I'm not 100% certain because i've never done this before. From what i saw it looks like you can either put that into your php.ini, or into a .htaccess.

AddType application/x-httpd-php .php .htm .html
//Tells the server to treat html and htm files as php files.

< FilesMatch "\.(php?)$" >
php_value auto_prepend_file "/the/path/that/leads/to/count.php "
</FilesMatch >
//Adds your adpage (e.g. /the/path/that/leads/to/count.php) to beginning of all php files.

Might not have everything perfect, but i think that's close.