Not provided trend past 12 months
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.
Browser forensics sheds some light
An analysis of the not provided ratio from a browser perspective provides interesting knowledge, the highest ratio of not provided referrals to this site occurs when visitors are using either Chrome or Firefox to click on a Google SERP link.
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 gained by the comparison, this site would benefit in this perspective to have more visitors using MS IE or Safari browsers in terms of reducing the not provided ratio.