The Google Webmaster Central Blog announced they have updated the verification tool to make it easier for webmasters to verify their sites. There are three main changes:
(1) New look for HTML file verification process:
(2) If you use the META Tag verification option and you change your email address tied to that Google account, the sites will now still remain verified.
(3) If you use the HTML file verification option, you no longer need to make sure your 404 pages actually return a 404 server status code.
With this update, some publishing tools no longer have the ability to verify their sites with Google Webmaster Tools, one example is Google Sites. Google is aware of this and working on addressing the issue.