Let's say, you have a subfolder on your domain that gets hacked. The hack causes your subfolder to be penalized by Google, due to the hack. Did you know that in order to issue a request for a review from Google in Webmaster Tools, you will need to individually submit and verify that subfolder to Google Webmaster Tools - even if you have the main domain listed and verified in Webmaster Tools?
A Google Groups thread discusses just that.
Googler, Susan Moskwa, explains:
If only a certain section of your site has been affected by malware (such as the /blog subfolder), you'll need to add that section specifically to your Webmaster Tools account in order to see the malware review notice. A great way to figure out which section(s) have been affected is to do a site: search and see which URLs have the malware label in search results.
Susan went on to agree with webmasters that it would be nice to be able to handle some of these requests at the top level domain, as opposed to having to register additional sub-directories or sub-domains with Google. But, as you can imagine, it makes sense why Google currently requires the individual registration - to handle third part hosting sites like Blogger, and so on. This is what Susan said:
I agree that it would be nice to bubble this up to the top level of the site (so that you can look at the Overview page for example.com and see that there's malware on example.com/blog), and I've passed your feedback along to our team.
Forum discussion at Google Groups.