I have been searching for a replacement for Google Notebook (RIP...) and have started using evernote. I LOVE the integration across platforms and cloud. However one thing i really miss from Google Notebook is the ability to add note sections within notebooks.
Although Evernote appears to be search heavy, i like to browse my notes sometimes when I am not looking for something specific. Sections helped me keep a visual organization and my notes neat. Ideally I would want to add sections and move notes into them, as well as leave notes, in a notebook without having to put them in a section (one thing onenote won't let you do). Perhaps the best way to allow users to organize their notes is make notebooks like system folders (ie. they could contain notes, folders or sections, and shortcuts to other locations).