Depends on the use case. If you are using it in as a website authoring tool, it makes sense to store the rich-edit user input as HTML itself.
However, in a scenario like commenting or composing a message (where only limited editing options are available), storing in a format such as Markdown make sense.
Not really what you're after, I guess, but a link anyway: http://code.google.com/p/pagedown/wiki/PageDown "PageDown is the JavaScript Markdown previewer used on Stack Overflow and the rest of the Stack Exchange network. It includes a Markdown-to-HTML converter and an in-page Markdown editor with live preview."
However, in a scenario like commenting or composing a message (where only limited editing options are available), storing in a format such as Markdown make sense.