A Google Groups thread has a webmaster who was very concerned when he logged into Webmaster Tools to find out that his site was not indexed by Google.
The reality was, it was indexed by Google, but Webmaster Tools showed the site not to be indexed by Google. Why did Google Webmaster Tools show the site not to have been indexed by Google? It is basically a feature. :)
JLH along with Googler, Reid, suggested the issue was with him not setting the preferred domain. Why is this an issue? Well, Reid said that he was looking in his Webmaster Tools report for the WWW version of his domain. But Google decided the non-WWW version was the primary site. So the Google Webmaster Tools reports showed that the WWW version was not indexed.
Googler, Reid, recommends that this webmaster to "verify the non-www version in Webmaster Tools and set the preferred domain to the non-www version." Reid said that will set the Google Webmaster Tools reports right.
This is an interesting thread because this issue really doesn't come up all that often. So if this does come up for you, this is your answer.
Forum discussion at Google Groups.