Google Webmaster Tools has a very powerful tool for SEOs, it is the links to your site report.
Ever since launching that report, Googlers and SEOs have been encouraging people to stop using the link command and use this tool. In fact, on the Google help page it said, "using the link: operator to find a sampling of links to any site." They then suggest you use the link tool within webmaster tools to get "a much larger sampling of links."
So when I spotted a post at Google Webmaster Help, I noticed a person complaining that the tool is only showing 1% of their real links. In response to that, Googler Pierre Far replied:
Keep in mind also that Webmaster Tools show a sample of links, but isn't guaranteed to show 100%. So some links may exist to either URL that aren't necessarily displayed in Webmaster Tools.
Pierre was not the first Googler to say this about webmaster tools, Susan Moskwa said it in March 2010, but I missed it then.
I am surprised that would be the response for a tool that shows a pretty accurate number of links. Google has been pushing people to stop using the link command and use this tool. If it is just a "sample of links" and not that accurate, what is the point?
This is a bit upsetting to me. Not that the link report might be not a 100% accurate but that Googlers are using the same excuse they used with the link command here with the link tool within Webmaster Tools.
Forum discussion at Google Webmaster Help.