A Google Webmaster Help thread has a report that someone noticed their site was verified in Google Webmaster Tools without them actually clicking the "verify" button. How did this happen?
Well, first of all, the www version of the site was verified. The non-www version they did not manually click verify for. So, Googler, Dennis G. explained in the thread:
Sometimes we can tell that you have a site verified even if it does not show up in your site list in Webmaster Tools. Usually this is because you verified the site a while ago and removed it from the list, or because the verification bot detected that its the same site (common for www/non-www URLs) and had the same verification tokens in place. That latter check doesn't happen in most cases any more, so you're more likely to have to explicitly add and verify the non-www site. You can then delete the site from Webmaster Tools if you like; we'll know you're still verified. On the other hand, sometimes there is useful feedback about your "other" site, so it's not a horrible idea to leave it there and check on it every now and then.
Pretty neat, at least I think so.
Forum discussion at Google Webmaster Help.