The nice thing about Markdown is that it’s a very lightweight markup language which lets you write files in any text editor which look pretty normal when read as plain text, because they use mostly the kind of idioms which people commonly use in text documents anyway, but you can run them through a simple converter to generate HTML or PDF output with all kinds of fancy formatting.
The not-so-nice thing about Markdown is that approximately seven seconds after its original creation, it split into a kazillion subtly different flavours, variants and dialects. There’s Original Markdown, PHP-Markdown (a.k.a. Markdown Extra), GitHub Flavored Markdown, Pandoc Markdown, and a whole bunch of others. So whenever you move from one tool to another, you have to learn and unlearn a few tricks, and fix some subtle breakage in any content files you try to take with you..
So, if you have free choice to pick any of the many command-line tools for converting Markdown to, say, HTML, which one should you choose? That one’s easy: Pandoc. It’s amazing. It can convert to and from pretty much every markup format ever invented. Its own default flavour of the Markdown syntax is incredibly complete (you can literally write books in it), and pretty much a superset of all of the others, but you can selectively disable features, or even put it into ‘strict’ mode where it will behave almost exactly like John Gruber’s original version.
The main disadvantage of Pandoc is that it’s addictive: after writing some documents in Pandoc Markdown, going back to one of the more limited variants feels like going back to a Punto after zipping around in a Ferrari for a while. This commonly happens when you are using a blog or wiki which lets users write pages in Markdown.
The obvious solution, if you happen to be the maintainer of that blog or wiki site, is to configure it to use Pandoc instead of some lesser Markdown-to-HTML converter. (If you’re not, you will just need to suck it up, I’m afraid.)