90% of 'links to your site' disappeared in Google Webmaster Tools

Its not just you. Here is a thread about the problem on WebmasterWorld: http://www.webmasterworld.com/google/4542427.htm

Here is a thread about it in the Google webmaster help: http://productforums.google.com/d/topic/webmasters/HB8ZdK_DDyw/discussion

This issue has been forwarded to Google engineers who are apparently looking into a problem with the webmaster tools.

Update: Search Engine Roundtable is reporting that Google has fixed this bug as of February 12, 2013. http://www.seroundtable.com/google-webmaster-tools-links-back-16349.htmlhttp://www.seroundtable.com/google-webmaster-tools-links-back-16349.html