Most of OJS 2.x's settings are stored in the database, particularly journal settings in the journal_settings table, and are accessed via the appropriate DAOs and Model classes. However, certain system-wide settings are stored in a flat file called config.inc.php (which is not actually a PHP script, but is so named to ensure that it is not exposed to remote browsers).
This configuration file is parsed by the ConfigParser class (classes/config/ConfigParser.inc.php) and stored in an instance of the Config class (classes/config/Config.inc.php).