The Google Webmaster Central Blog talks about how you can use Google Webmaster Tools to learn about problems with your site. In the post, JohnMu (yes, that John) explains the variety of issues you can run into when you have an IIS server and are returning the wrong status codes. He also says that you can find out if there are broken links by reviewing the "Web crawl" area of Webmaster Tools and explains that some of these issues are not easily spotted.
John looks into other issues as well, including redirection issues, server unreachable errors, and even if your web site has been hacked. He explains that Google Webmaster Tools can give you more information about this and other common errors.