As promised new version is available. Google Query Stats Tool V2
Google provides webmaster tools which are extremely useful to analyze your website, particularly its performance on google searches. It provides all sorts of data from external links to your webpages to index stats, crawl stats, diagnostics etc. It provides all sort of data to download relating to your website.
One such dataset is Top Search Queries. These are the queries in which your website figured in top results. This data is categorized for locations, search types as well as for your web pages or sub folders. You can download this data in csv format. Although you can view this data online for your main site but you are not able to look at the complete data including sub folders on the google webmaster tools website. Using this GoogleQueryStats tool you will be able to do that offline.
You may need to install dot net framework 2.0 if the exe complains.
Come back as the next version of this program will make it possible to compare search queries from different periods.