I know I am pretty much stating the obvious here, but there is a DigitalPoint Forums thread where Google AdSense publishers are discussing their click through rates for the search ads.
Some range as high as 7% as discussed in the thread. But some range as low as under a half of a percent. What makes for the difference?
Looking at my own data. I can tell you my personal blog received a much higher click through rate on its custom search engine then does this site's custom search engine.
Why? I believe because more normal people are visiting my personal blog versus this site. By normal people, I mean people who are not involved in search on a day to day basis. I have friends, family and random searches come to my personal blog. Whereas this site gets a lot of traffic from search professionals.
There can be many reasons why one site would have a higher click through rate (CTR) on the search ads when compared to the next. They include, but are not limited to, audience, design, type of search, traffic, layout and much more.
Forum discussion at DigitalPoint Forums.