More data and charts in Top Search Queries
googlewebmastercentral.blogspot.com
googlewebmastercentral.blogspot.com
However, as it stands, my digging suggests that not only are the numbers dramatically different between other sources and GWMT, they're not even consistently different (at times, the multiples of variance can range from 0.5X-3X).
A number of good posts have been written on this by the webmaster/SEO community already:
http://www.distilled.co.uk/blog/seo/new-google-webmaster-too...
Line-by-line comparisons seem to hold up pretty decently, though, in my five minute spot-check.
0.01% (12 clicks out of 110000 impressions)