Editing Tools

What WYSIWYG tools exist for markdown today?

Editorially is a new product mainly for collaborative writing. Hides the markdown a little bit. You can enter it or use a toolbar.
MarkdownMail for iOS
Multimarkdown
WYMeditor
MOU
Epic Editor (JavaScript oriented)
Markdown Pad (Windows)
35+ Markdown apps for the mac: http://stefgonzaga.com/2012/11/markdown-mac/

Citations
Figure metadata
Tables are messy
Math is not such an issue if you wrap LaTex or MathJax
Pandoc (command line tool to convert markdown to HTML, XML, PDF, etc.) could be hooked in for outputs and rendering
It may need a local instance to solve the psychological security of writing locally vs. writing in the cloud
- In this case the idea of packaging the paper's files comes into play (figures, etc.) the way something like knitr can do
Track changes and comments (a real solution, not what GitHub can offer). CriticMarkup does this but via markdown - it's not enough
http://blogs.plos.org/mfenner/2012/12/18/additional-markdown-we-need-in-scholarly-texts/

Many science publishers archive XML for the long haul - how can markdown address this? Strictly by transforming to NLM at the end of authoring?
We suspect markdown will be more human readable than Word in 100 years

We believe that a strong percentage of smart authors will need to see a visual representation of their writing in order to be comfortable in an authoring environment, so yes.
But a good thing about markdown is that formatting is not at all a consideration.
One of the problems of a WYSIWYG editor is about copy/paste from Word. Either allow only plain text paste or you have to clean it up. WYSIHTML5 does a good job with copy/paste from Word.

The more you move towards an editor that will hide the Markdown, the less it makes sense to use Markdown in the first place.
Ideally, for whatever format the industry adopts, it must be a simple thing, possible to pick up the basic functionality immediately and intuitively, and learn the advanced features over time.