I've noticed that some of my websites the results for the total number of indexed URLs is pretty close to what I get for a Google Site Search (site:mywebsite.com). However on some of the sites, it's off by a factor of 2x or greater. Anyone have any insights into this? For example: Google Site Search. "site:mysite.com" - About 5,000 results. Google Webmaster Tools. Web Indexed: 2,500
Google searches for your website, i.e. site:yoursite.com gives broader results compared to WMT.. It shows, pages, posts, categories, tags etc.