I just cleaned up my Evernote notebooks, going from a notebooks for each company I’m involved with, plus notebooks for Skitch screenshots, files, etc., to having just two: “Inbox” and “Notes.”
The only reason I’d have more, is to share or collaborate; however, I’ll mostly be using Evernote for Business to do that, so that will offer some separation.
Another notebooks you may want to have if you do GTD or similar, is a ”Projects” or “To Do” notebook—but I’m integrating all my todo’s into actual notes in the single “Notes” notebook. Have not yet documented my new system (which I call the Triple-M, or “Mental Model Method” system), but it involves smart use of Evernote search to make things as simple as possible, and mimic how your individual mind already naturally organizes information—something that’s very subjective.
(For example: you can view any notes that contain unchecked checkboxes by searching for “todo:false”. Very nice, and makes Evernote extremely flexible.)