I read an article on the Evernote blog last week that provided some tips for cleaning up your digital life and Evernote. I have been using Evernote heavily for the last several months and it has added an incredible amount of organization to my life.
I took a cue from the article and decided it was time to clean things up a bit. I eliminated all of the stacks that I was using. My initial thought was that they would be a great way to organize notebooks, but found that they tended to prevent me from finding what I wanted and cluttered things up more than they helped. One of the strengths I see with the Evernote interface is that there is only one level of organization above the note, the notebook. Many users have asked for unlimited levels of notebook aggregation, similar to files and folders on your drive. Not to say that anyone would have to use it if the feature was implemented, but I think it would take away from what Evernote is and prevent many users from finding the magic.