I prefer storing the markdown so you can parse it or show it as it is when editing the post.
And as a response on the second question, it depends on what you are building, if you are creating a site for developers using a markdown is fine, but if you are building a site for normal users i prefer using WYSIWYG-editor and storing the post as HTML.
I would prefer storing the content in markdown format as well, but I don't want my clients (non-devs) to learn the markdown syntax. They mostly use MS Word, thus they know how to format text by selecting it and click the [b]old-icon to make it bold etc.
What are you feelings and/or experiences with "teaching" markdown to non-dev clients?