The ability to analyze SEO combined with search terms has given many webmasters a better understanding of their visitor traffic as well as improving it. However the massive increase of "(not provided)" is for websites with most of their search engine referrals from Google a real issue.
On this website the ratio of not provided has from May 2012 grew from ~30% up to ~65%, which at this point is making search term analysis pretty useless when looking at the total volume of visitors.
Many analysts have suggested a slew of alternative methods, but they are at best only going to give an extrapolated view of the search terms with a most certain degree of incorrectness.
What is very evident is that (not provided) is an increasing issue that cannot be solved with any universal solution, no matter how ingenious. Also it means that any comparison with search term data in the Google Webmaster Tools is rather useless.
Not provided is caused by the use of secure search which means that these visitors very likely were logged into a Google service such as Gmail.
A very obvious conclusion is that the popularity of the Google services will strongly have an effect on web analytics with regards to search term analysis and SEO.
In light of this conclusion and the browser related insight, this site would benefit in this perspective to have more visitors using MS IE or Safari browsers.
What is little known and written about is that Google handles cookies in a quite dirty fashion. When logged in to the Google.com domain using another Google domain such as Google.se means that I will automatically be redirected to the secure search this despite using another domain. That in my book is "doing evil" as well as being a major contributor to the not provided issue.
It seems that it's time to start sending Google a message, with the same volume as it is being dished out, that (not provided) really sucks...