This is a late comment, but hopefully still useful. In the 25 Feb "Things I Think I Think" Mark talked about switching to byword and using markdown for show notes. I am a Markdown evangelist at work, so I was excited for everyone at Manager Tools who switched with him (presumably Mike did, as well).
I have a short note for how I use markdown. Maybe it will be helpful in a small way.
Byword: I keep active documents in iCloud and move them to Dropbox for storage and reference. For all its problems, iCloud is great for syncing small text files. Since byword lives on both OS X and iOS, it is easy to pick up where I left off regardless of where I am.
Marked 2: This is for previewing and exporting markdown on the Mac, but that really undersells it. It is a critical tool for me for writing in markdown. It has readability statistics, viewing options for long documents, the ability to export OPML for a mind-mapping program or omnioutliner, and the ability to generate html with your own css.
Nvalt: This is a fork of notational velocity on the mac. I have it pointing to the Dropbox folder that I move my byword files to. It is a tool for quickly creating and searching files. This sounds basic. You have to work with it a little to see how it removes friction from a markdown-based workflow. There is an overview here
Markdown Service Tools: This is a number of OS X services that are developed to make writing in markdown easier. There are a lot of them, here is one that I use as an example
Links - New Link
This will surround the selected text with inline link syntax, and if there’s a single url in the clipboard, will link it automatically. Otherwise, it will create a shell ([link text]()) with an empty parenthesis pair for you to paste a url into.