Another reason to be careful who gets webmaster tools access. A disgruntled ex-employee with access can do a lot of damage to a site. Re-target the site to a small island nation, or now remove key pages from the index.
When my site loses traffic, one of items on my checklist is now webmaster tools. Just to make sure nobody's fingers slipped on any of the controls. I haven't figured out ways to make sure QA monitors it. Its not as easy as "Make sure page X is crawlable, linked from the home page, and contains 'keyphrase' in the title".