I have no real preference either way, but personally I use Markdown a lot in ruby and also in my local files.
I do not even use markdown directly for ruby, but instead have a template ending with .gen, and a ruby script then expands this with more information when I upload a gem in ruby. What is really awesome with markdown is that it is so simple, and you can get some simple "styling" too. And you could even use HTML bold tags like <b> too, rather than two stars ** - so it allows for a bit of flexibility. (HTML) Tables are also quite easy to do in markdown. I like markdown a lot. I don't mind other forms of documentation but for me personally, Markdown is awesome. It's not perfect for all cases though. I think some websites may need more control over their content. For example functionality such as "show source code of a method" \- that would be pretty difficult with markdown as such (ok ... not really possible right?).
