When comparing Emacs Org-mode vs Jupyter, the Slant community recommends Emacs Org-mode for most people. In the question“What are the best tools for Literate Programming?” Emacs Org-mode is ranked 2nd while Jupyter is ranked 4th. 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
Ranked in these QuestionsQuestion Ranking
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 Web-based development allows for usage literally anywhere
Because the editor is a web app (the Jupyter Notebook program is a web server that you run on the host machine), it is possible to use this on quite literally any machine. Morever, you can have Jupyter Notebook run on one machine (like a VM that you have provisioned in the cloud) and access the web page / do your editing from a different machine (like a Chromebook).
Pro Interactive
Most IDEs require you to separately run Python to see the output of a particular piece of code. By contrast, Jupyter Notebook can evaluate Python statements inline, giving you the immediate feedback of interactive use of the interpreter while keeping your changes saved.
Pro Graphing , charting, and other math/numeric capabilities
The interactive editor is able to display complex equations, charts, graphs, etc. making this particular editor very well-regarded among data scientists.
Pro Open source
Because it is open source, you can review the source code and also propose extensions and fixes to it. It is also possible to fork the repository and make changes to it to customize it for your specific use case.
Pro Supports multiple different programming languages
Jupyter Notebook, formerly known as ipython, used to be specific to Python; however, in recent iterations, it has become capable of general purpose usage for any programming language. Thus it is possible to use this and have a consistent developer workflow, regardless of language.
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 Notebook-style makes reusing functions annoying
Con Interactive usage takes some getting used to
While the interactiveness is extremely, extremely powerful and useful, it does take a little bit of work getting to a point where it is "normal".
Con First time setup is more difficult than for other IDEs
Since Jupyter Notebook really requires two programs (the server and your browser) getting things setup in a way that works for you is a little more complex than for an ordinary IDE. For example, if you run the server and edit on the same machine, creating a little wrapper script that starts the server and then launches the browser pointing to it and gives an icon to this script is a small amount of setup but is more involved than a simple installer for other IDEs. Likewise, if you do remote development, creating a URL that will lazily spawn the Jupyter Notebook server and then turn it down when it is no longer in use is also a little bit of work to setup.
Con Non-trivial security configuration for remote access
By default, the editor is only accessible from localhost; however, if you want to run Jupyter on a VM in the cloud and do your editing through a web browser on a different computer (e.g. a Chromebook), there is some non-trivial security work to ensure that it is set up in a secure manner.
