Deny direct access to all .php files except index.php

Are you sure, you want to do that? Even css and js files and images and …?

OK, first check if mod_access in installed to apache, then add the following to your .htaccess:

Order Deny,Allow
Deny from all
Allow from 127.0.0.1

<Files /index.php>
    Order Allow,Deny
    Allow from all
</Files>

The first directive forbids access to any files except from localhost, because of Order Deny,Allow, Allow gets applied later, the second directive only affects index.php.

Caveat: No space after the comma in the Order line.

To allow access to files matching *.css or *.js use this directive:

<FilesMatch ".*\.(css|js)$">
    Order Allow,Deny
    Allow from all
</FilesMatch>

You cannot use directives for <Location> or <Directory> inside .htaccess files, though.

Your option would be to use <FilesMatch ".*\.php$"> around the first allow,deny group and then explicitely allow access to index.php.

Update for Apache 2.4:
This answer is correct for Apache 2.2. In Apache 2.4 the access control paradigm has changed, and the correct syntax is to use Require all denied.

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