You don't (easily).
There are both open source and commercial directory and file encryption programs out there. You can run one on your server.
But unless you manually decrypt the encrypted file or directory as you start your system (which means the password is going to be held somewhere) apache is just going to send the encrypted file or directory across the 'net and you'll have to manually decrypt it locally.
You can encrypt and decrypt data stored in mysql, and move it across the net through PHP.
Jeff