The Site application, also known as the Front-end, is the main part of a Joomla website. This is where the general traffic occurs: when a visitor uses your site, he will be using the Site application. You can manipulate this (add/remove content, switch templates etc.) from the Administrator application.
The Site application is implemented in the JSite class, which is a subclass of the generic JApplication. The JSite object can be retrieved in all versions that support JSite using the following code. The application will be a JSite object when this code is run in the Site application.
$app = JFactory::getApplication();