You should name your classes so the underscore (_) translates to the directory separator (/). A few PHP frameworks do this, such as Zend and Kohana.
So, you name your class Model_Article and place the file in classes/model/article.php and then your autoload does...
$filename = str_replace('_', DIRECTORY_SEPARATOR, strtolower($class_name)).'.php';
$file = AP_SITE.$filename;
if ( ! file_exists($file))
Also note you can use spl_autoload_register() to make any function an autoloading function. It is also more flexible, allowing you to define multiple autoload type functions.
If there must be multiple autoload functions, spl_autoload_register() allows for this. It effectively creates a queue of autoload functions, and runs through each of them in the order they are defined. By contrast, __autoload() may only be defined once.