Which markup language should you be using? Org or Markdown?
First, let us begin with their inception. Org is a markup language and major mode for Emacs. It can be used for note-taking, scheduling, journaling, literate programming, book-writing and more. The markup language is extensively used in the Emacs ecosystem, becoming very modular and tightly integrated because of it.
Markdown was created by Aaron Swartz, one of the founders of Reddit. It was created to be “an easy-to-read and easy-to-write plain text format”. It is mainly used online for formatting on blogs, comment sections and social media websites, but its popularity led it to become adopted by developers in other programs such as Jupyter (Notebook) and various note-taking apps.
Which one should you choose? Well, I cannot decide for you, but I will make it easier for you. Org and Markdown, as markup languages, are not that different. Although, there are other deciding factors.
Markdown is more popular than Org. There are more parsers and more applications that support it as a formatting option. Its popularity is similar in nature to markup languages such as BBCode.
Org is a lot less popular, resulting in less programs supporting it. In fact, I would be surprised if any website supported Org formatting. Although, Org is very tightly integrated in Emacs, making it very easy to string different things together, but you will be forced to use Emacs for pretty much anything involving Org if you want everything to be tied together beautifully.
In conclusion, I would say that using Org outside of Emacs is a stubborn choice, and most of the time not even an option.