[jcynix]

Markdown is a markup tool, i.e. you decorate your text. Orgmode on the other hand is a complete toolbox where you can add tags to notes, filter on these tags, manage calendars, etc. You can enter tables both for formatting and spreadsheet like calculation.

And you can insert snippets of code into your notes, like

    #+BEGIN_SRC shell
       ls | wc -l
      find . -type f -name "*foo*" 
    #+END_SRC

(or javascript, elisp, html, ... instead of shell) where the markup is changed appropriately in these regions.

You can even augment orgmode with elisp code if you are so inclined.