Markdown is a great way of writing HTML, but every implementation is slightly different. But perhaps not any more. CommonMark aims to prepare a definite Markdown syntax that can be used anywhere. Now Markdown is being used everywhere from README files to content management systems, this can only be a good thing.
Update (9 Sep 2014): CommonMark was originally known as Standard Markdown. The name was changed at the request of John Gruber, the original creator of Markdown. I have updated the text and link here with the new name and URL.