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Are you missing the query data (the searched words) in Google's referrer links?
There used to be a time when the HTTP_REFERER string contained the information what a user was "googling" for. Looking at the traffic I can see that this is gone in many requests.
The announcement came in October 2011 and the impact on the query string was not quite obvious in this brief statement.
The change as it stands right now happens only when somebody searches over SSL, i.e. if a user uses https://www.google.com for searching. In all these cases the URL will be altered in the submitted HTTP referrer string.
Although you can still see that the traffic came via a Google search you can say Bye-bye to search terms in the link.
This also causes some changes in the statistics you have with Google Analytics. Because it works only on the client it can only inspect the referrer and not the Google website itself.
As much as you are missing now the keywords in your logs you will be missing them in Google Analytics.
There is little hope with the Webmaster Tools but quite frankly it was never really that informative since it only shows some top keyword strings and not a complete list of everything.
Overall I am afraid we have to get used to it and we will see probably even more restrictions. I wouldn't be too surprised if this will be extended to any type of search at some point in the future.