Wordpress: difference between site_id and blog_id?
site is a reference to a network of blogs. There are efforts under way to allow WordPress to support multiple networks in addition to multiple blogs, but right now that's not a stock feature (which is why the wp_site table only contains one value.
The wp_blogs table contains all of the blogs for your entire installation, with each identified by the site it's associated with.
This gives you a clean separation between networks, and (eventually) you'll be able to have different "groups" of blogs on one WordPress installation behave like distinct multisite installations.