I find that markdown is good for 'simple' human readable things, but that parsers can often fall on their faces.

A particular issue I have with markdown is the bold/italic issue. However this is probably indicative of a broader issue. Markdown either does not have, or does not commonly make users aware of, an escape character which will always invoke a control-word boundary and which will never be rendered in the final text.

I've also often had different websites variations on features fail when they are nested (sometimes at all).