way different stats in Analytics and Webmaster tools
 

WTF, I have been checking my analytics stats every day and see I am averaging only two google hits a day. (up from one a day so I'm sadly kind of pleased with that)

Now I check the same site in Analytics (for the first time) and I am on page 1 for a couple search terms I was targeting and am getting about 1000 times more google love than analytics will admit.

Why such a huge difference?

google analytics isn't very accurate, for accurate stats you want something that runs on the server log files. Awstats, for instance.