If you try to download the top query report from Google Webmaster Tools you will be out of luck.
There is a bug that is preventing the data from being downloaded as a CSV file.
At the bottom of the top query report in Google Webmaster Tools there is a link to "Download this table." Clicking it will in fact download a file but the file will be pretty much empty.
A Google Webmaster Help thread has reports of the issue and Googler Jonathan Simon from the Seattle office confirmed the issue, he said:
We're aware of the issue of the "top queries" download not currently including the expected data. We're working on restoring the download functionality as soon as possible. Thank you for reporting this issue here in the Forum.
There is not ETA for a fix, but I don't expect it to take that long.
Forum discussion at Google Webmaster Help.