Are the files on the same server as the PHP script? If so, just keep the files out of the web root and make sure your PHP script has read permissions for wherever they're stored.
The safest way is to put the files you want kept to yourself outside of the web root directory, like Damien suggested. This works because the web server follows local file system privileges, not its own privileges.
However, there are a lot of hosting companies that only give you access to the web root. To still prevent HTTP requests to the files, put them into a directory by themselves with a .htaccess file that blocks all communication. For example,
Order deny,allow
Deny from all
Your web server, and therefore your server side language, will still be able to read them because the directory's local permissions allow the web server to read and execute the files.
If you have access to you httpd.conf file (in ubuntu it is in the /etc/apache2 directory), you should add the same lines that you would to the .htaccess file in the specific directory. That is (for example):
Do this for every directory that you want to control the information, and you will have one file in one spot to manage all access. It the example above, I did it for the root directory, /var/www.
This option may not be available with outsourced hosting, especially shared hosting. But it is a better option than adding many .htaccess files.
in httpd.conf to block browser & wget access to include files especially say db.inc or config.inc . Note you cannot chain file types in the directive instead create multiple file directives.
<Files ~ "\.inc$">
Order allow,deny
Deny from all
</Files>
How about custom module based .htaccess script (like its used in CodeIgniter)? I tried and it worked good in CodeIgniter apps. Any ideas to use it on other apps?
<IfModule authz_core_module>
Require all denied
</IfModule>
<IfModule !authz_core_module>
Deny from all
</IfModule>