In Google Webmaster Help there is a straight forward question and answer about how to handle M-dot (i.e. m.domain.com sites in Google Webmaster Tools.
In short, an M-dot is a separate site and should be verified separately in Google Webmaster Tools.
Zineb, a Google Webmaster support representative answered each question:
(Q) Having verified domain ie.http://www.domain.com in GWT do I need to separately verify it's mobile version ie. m.domain.com? If so which method is the best for mobile?(A) Yes. You need to verify both URLs in Webmaster Tools. Regarding verification methods, it depends on what you prefer :)
Furthermore, she answered the question on a separate mobile domain.
(Q) Also if the mobile website will have different URL ie. m.domainmobile.com how will that affect the verification (obviously having verified http://www.domain.com wouldn't help).(A) I don't see why it would affect the verification. Make sure to add the bidirectional annotation to both your sites (mobile and desktop) to help our algorithms understand the relationship between your desktop and mobile pages.
Forum discussion at Google Webmaster Help.
