I can set the PHP include path in the php.ini
:
include_path = /path/to/site/includes/
But then other websites are affected so
Why do you think append to include path is bad practice?
This code near top of root script shouldn't be that bad...
$path = '/path/to/site/includes/';
set_include_path($path . PATH_SEPARATOR . get_include_path());
IMHO the main advantage is that it's portable and compatible not only with Apache
EDIT: I saw a drawback of this method: small performance impact. see http://www.geeksengine.com/article/php-include-path.html