When comparing Emacs Org-mode vs Notebooks, the Slant community recommends Emacs Org-mode for most people. In the question“What is the best note taking app for Mac?” Emacs Org-mode is ranked 18th while Notebooks is ranked 20th. The most important reason people chose Emacs Org-mode is:
This app's flexibility is based on its minimalist approach, giving the user near-infinite freedom.
Specs
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Pros

Pro Ultimate flexibility
This app's flexibility is based on its minimalist approach, giving the user near-infinite freedom.
Pro Absolutely free
Emacs with Org-mode is free as in beer and free as in speech – that is, it costs nothing and it’s totally open source.

Pro Files are usable anywhere at anytime
Users are not tied to one service provider, program, platform, or database engine.

Pro Incredibly extensible
There are many plug-ins for Org-mode, including Org-habits and Org-notify. If Org-mode lacks some piece of functionality, it is very easy to add it.
Pro Agenda views
Pro Excellent unofficial Android app (orgzly)

Pro Offline support
Pro Efficient features for deadline organization
Pro Supports plaintext spreadsheets
Pro There are a lot of extensions, for exporting to html, bootstrap, js-reveal and much more
Pro Quickly add rich text
Pro You control how to sync the data - better privacy
Services like Paper (Dropbox), Evernote, Google, OneNote (Microsoft)... and many others, keep your data in format they can read when it syncs with their servers. That means their admins can read your data (see recent scandal with Evernote privacy policy), they can be compelled to give it to law-enforcement and, if hackers manage to breach their servers, the hackers can read it too.
With Notebooks, you choose how to sync your data, which means that you can do it using a privacy-friendly service, such as SpiderOak, Tresorit, Sync.com or iDrive, which sync your data using end-to-end encryption. This means that although they use their servers to sync your data, their servers store an encrypted version to which the service does not hold the key. Your data stays private.
Pro Powerful and grows according to your needs
Notebooks have many features including WYSIWYG editing and Markdown support. While these may be considered power-user features, they are there if the user ever needs them. This makes the app versatile, as it can appeal to the user who just wants to take notes just as much as the user who needs to edit complicated documents.
Pro No recurring fees
There are no reoccurring fees connected to this app: pay once for the platform you would like to use it on, and that's it.
Pro Available on multiple platforms
As an Evernote alternative, Notebooks is available on iOS as well as OS X and Windows operating systems. This makes for a convenient way to manage one's notes or tasks on multiple devices
Cons
Con Unintuitive user interface
The key combinations are unintuitive and difficult to remember. This is probably because there are a lot of hidden "modes" depending on where the cursor is. Actions aren't paired with reversing actions like in other todo apps. For example, hitting shift-tab does NOT reverse the effect of hitting tab.


Con Android app isn't very good
There are several user-created apps for Android, but none seem to offer the same level of functionality as other to-do apps.
Con Not really cross platform
Although it is possible to get a lot of it working, no all in one, sync included, out of the box solution is available for mobile devices.
Con By default, a hard-to-read display
The default way of writing an outline or checklist creates a very messy wall of text that's difficult to read with no vertical spacing. You can manually add vertical spacing, but the Org operations don't preserve it. There are pretty-display modes, but you need to remember how to enable them, etc. etc.
Con No Linux support
Not able to install on any Linux-based OS.
Con Each platform app has an individual cost
Say if you want to use the desktop app on OSX, that will have an individual cost. This cost does not carry over if the Windows app needs to be used as that has its own cost as well. Basically you have to pay for each platform you want to use this app on. While there are no recurring fees, the individual cost for each platform can add up.
Con Cloud sharing has to be done with a third party
Notebooks does not provide its own synchronizing and back-up. The user will therefore need to use a service (such as Dropbox) which has built-in support, but which is a service not connected with the creators of this app.
