Here's a comprehensive look into the new features.
Up to 6 months of historical data:
Previously we only showed query stats for the last 7 days. Now you can jump between 9 query stats snapshots ranging from now to 6 months ago. Note that the time interval for each of these snapshots is different. For the 7 day, 2 week, and 3 week snapshots, we report the top queries for the previous week. For the 1 to 6 month snapshots, we report statistics for the previous month. And still others of you who log in may notice that you don't have query stats data going back to 6 months ago. We hope to improve that experience in the future.
Top query percentages:
You might have noticed a new column in the top query listings. Previously we just ranked your query results and clicks. While useful, this didn't really tell you to what extent one query was ranked higher than another. Now we show what percentage each query result or click represents out of the top 20 queries. This should help you see how well the result or click volume is distributed in the top 20.
Since we're now showing historical data on the Top Search Queries screen, we figured it would be rude to not let you download it all and play with the data yourself (spreadsheet masochists, I'm looking at you). We added a "Download data" link that lets you download all the stats in CSV format. Note that this exports all query stats historical data across all snapshots as well as search types and languages, so you can slice and dice to your satisfaction. The "Download all stats (including subfolders)" link, however, will still only show query stats for your site and sub-folders for the last 7 days.
We've improved data freshness in Webmaster Tools a couple of times in the past, and we've done it again with the new Top Search Queries. Statistics are being now updated constantly. Top query results and clicks may visibly change rank a lot more often now, sometimes daily.
More information available in the Google Webmaster Central blog.