The company announced that, starting immediately, it will encrypt the searches that users conduct but only if the search originates from the main Google.com page and only if the user is logged on to a Google account at the time. Danny Sullivan of Search Engine Land talked to a Google engineer who estimates that this will affect a single digit percentage of searches since so many people search from an address bar on their computer. Also, when you click through on a result, the site you referred to will no longer be able to learn what you were searching on that guided you there unless they are an advertiser. This seems likely to really mess with the idea of search engine optimization (SEO) or at least challenge the thinking in that regard.
Even though SEO traffic in general can still be tracked, those who are doing conversion analysis down to the keyword level will begin to lose out. You wouldn't be able to tell, for instance, where someone coming to your site after finding it for a search for "blue widgets" actually entered, nor the other pages they viewed.
Another issue is that landing page targeting gets harder. For example, many have probably been to blogs that might welcome them with messages like:
Hello -- I see you came here from Google after searching for "blue widgets." Here are some stories about that topic you might also be interested in.
Without search terms being passed along, this type of basic targeting can't happen. It also prevents much more sophisticated targeted from being used.