Google announced you can now export many of the reports from Google Webmaster Tools directly into Google Spreadsheets.
Previous, you were able to export these reports as CSV or use a Python scripts or the API to export data from the tool.
Googler, Pierre Far, said on Google+:
To export the data, click the download data button and a “Select Download Format” option box will pop up where you can choose to download the data as “CSV” or “Google Docs.”
Forum discussion at Google+.