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.