Then, there is the 'clickability' of the listing - does it read well or not?
A poorly written title for a site - might lower it's CTR versus the number of impressions it got in the natural SERP's, even though it may have the 1st position, the #2 spot might outpull.
Also, the number of links at the top -> are bound to have an impact. Are there 0, 1, or 2 premium listings for 'keyword x'?
Start by nailing down the variables, & then continue with mining your log files. That is my method, and it seems to work well enough. :)