Google announced a new application, a Python script, that lets you download all your search queries available from Google Webmaster Tools.
Google is offering this for two reasons:
(1) They don't have the ability to download search query data via the Google Webmaster Tools API - yet.
(2) They removed about 10% or so of the search queries that show in your analytics when moving to SSL search and that will just get worse over time.
For more details on how this script works, see the Google Webmaster blog.
Google's John Mueller said on Google+:
If you haven't messed with Python, here's your chance to do something cool with it -- download the search queries data from your Webmaster Tools account, and automatically upload it as a Google Spreadsheet for your long-term logs.
Python isn't that complicated (if you're used to basic programming :-)), you just have to watch out for the indenting. Once you get used to it, it's really fun, powerful, & simple!
Forum discussion at Google+.