In the WordPress user interface, a site can simply be the website created by WordPress, or it can be a virtual website created as part of a network by the multisite feature. A site in a network is virtual in the sense that it does not have its own directory on the server, although it has its own URL and it might have its own domain name.

In WordPress code the site is the website created by WordPress. If multisite is in use, then the site is the network website and each virtual website is known as a blog.

Reference http://codex.wordpress.org/Glossary