In Google Webmaster Tools (Internal Links)

[raj1094]

Dear Webmaster,

In GWT under "your site on the Web" we have an option of Internal links. There we have option to select "From" as http://www.site1.com and the other as http://*.site1.com, what is the difference between these two urls in selecting the internal links.

[tedster]

The second option would include any kind of subdomain (hostname) - not only "www".

[raj1094]

Thank you

[g1smd]

Make sure you register both "www.example.com" and "example.com" in WMT.

Check both sets of reports. One of them will be almost empty, but there are a few interesting things to watch out for, not least the notification of other sites linking to the non-canonical version.