Other people have pointed out that most of the power comes from using Emacs. However, speaking as someone who used to use Notepad++ and Markdown, and now uses

Other people have pointed out that most of the power comes from using Emacs. However, speaking as someone who used to use Notepad++ and Markdown, and now uses Emacs and org-mode, I do think .org is a slightly better markup syntax. I can't quite put my finger on it. For some reason, Markdown seems great for a page or two, but gets irritating if I try to write longer documents. Possibly it's just a matter of editor support for treating it as a tree and letting you move bits around. Also, the tables in org-mode are really good.