It is hardly difficult to guess from the name itself that Google Webmaster Tools is a set of tools for webmasters. However, what you don't know right away is that this is a very useful toolset that allows you to communicate with Google and adjust many aspects of how Google sees your site, such as list the external and internal links to your site, adjust the crawl rate at which Google bot indexes your site, check the keywords users typed to land on your site, as well as the click through rate for each keyword, see your site's statistics, and many more.
One issue that needs mentioning is privacy concerns. Since you are giving Google a full access to your site's stats, you might be worried about how they handle this data. While Google is a reputable company and it is not very likely they will abuse the data you are giving them access to, if confidentiality is a top concern for you, think twice before letting Google (or any other statistics solution, for that matter) to your site's secrets.
If you use Google Webmaster Tools together with Google Analytics, the results will be even better. You can access your Google Webmaster Tools data directly from Google Analytics, so if you are already using Google Analytics, with just some more effort you could easily integrate it with Google Webmaster Tools, too.
