See Download File Structure Documentation (as of December 2007) and my Guide to Google Webmaster Central Tools and Downloads.
Query Stats Tool for Windows Desktop
Here is the page with the download link. I posted a comment there already (it is a forum or blog) and recommended some additional features to be added that would be very helpful. If the downloads on that other website becomes unavailable for some reason, use the following links to the copy of the tools on my own server as backup. GoogleQueryStatsV1.zip and GoogleQueryStatsV2.zip, each is less than 10KB in size.
Version 2 has a feature to compare to reports with each other, but some of the existing features of version 1 were dropped as a result of this (due to incompatibility). I suggest checking out both version to find out, which one works best for your specific needs.
Requirements: Windows XP or Vista and Microsoft DOT NET Framework V2.0.
Also useful: This Guide by Amit Banerjee about "How to Organize Search Query Data from Google Webmaster Tools in Excel".
What is this tool good for?
Site,Location,Search Type,Top search queries,Top search query clicks http://www.url.com/,(country) google.xx,search type,"[key phrase one:1][key ""phrase two"":2]",
You see, all Key Phrases for the same Site/Location and Search Type are grouped together in one cell, using "[,],:" and double quotes.
Site,Location,Search Type,Top search queries,Top search query clicks http://www.url.com/,(country) google.xx,search type,"key phrase one",1 http://www.url.com/,(country) google.xx,search type,"key ""phrase two""",2
Update December 2007: The word is out that Google is planning to do something about this query stats download, which will make this tool more or less obsolete. There is no date set yet, but it is estimated to be introduced within the first quarter of 2008. A real API to access the data directly and via automated means is also on the horizon. Hallelujah.
The tools supports various delimiters and text qualifiers. Here are the details (if you think that I missed one, let me know)
Here is an example of the Query Stats file, but Pipe delimited with no text qualifier instead of the CSV format:
Site,Location|Search Type|Top search queries|Top search query clicks http://www.url.com/|(country) google.xx|search type|key phrase one|1 http://www.url.com/|(country) google.xx|search type|key "phrase two"|2
For information and news to Google Webmaster Central and additional tools and services provided to Webmasters by Google via the portal, visit the official Google Webmaster Central Blog.
Google Query & Links Stats Converter API
The converter is based on the downloads as of Spring 2007. Some additions and some changes occured since then. See the documentation of the download files available at Google WebmasterCentral as of December 2007.
If you want to automate the process, use the API of my Google Query and Link Stats File Converter Tool instead. No XML or fancy Web Service. It is really simple and straight forward.
Examples for API Calls
Tab delimited stats with cr+lh line breaks for Windows and no need for text qualifiers
http://www.cumbrowski.com/googlestatsconverter.asp?url=http%3A%2F%2Fwww%2Eyoursitec%2Ecom%2Fgooglestats%2Ecsv&stats=3&rowd=crlf&cold=tab&txtq=clearURL with location to the stats (ficticious): http://www.yoursite.com/googlestats.csv
stats: 3 (All phrases for the Site)
rowd=crlf - Carriage Return and Linefeed
cold=tab - Tabulator character, practical for internet marketing, because "Tab" does not exists there.
txtq = clear, no text qualifier please
Much shorter URL, because advantage is being taken of the default options by not specifying them at all.
http://www.cumbrowski.com/googlestatsconverter.asp?url=http%3A%2F%2Fwww%2Eroysac%2Ecom%2Fg%2Ecsv&stats=3URL with location to the stats (ficticious): http://www.mysite.com/123googlestats.csv
stats: 3 (All phrases for the Site)
rowd=(none) = Default
cold=(none) = Default
txtq=(none) = Default
Free Query and Link Stats File Converter Tool (c)2007 by Carsten Cumbrowski