I’ve only recently started using Markdown, but CriticMarkup looks like a useful, non-trivial extension to the syntax. Compatibility with HTML and even LaTeX should make it especially versatile. Hopefully my writing and editing friends will weigh in as the project evolves!
From the linked review:
For someone who writes in Markdown and works with a team on a daily basis, CriticMarkup is the missing piece of a puzzle that required using clunky software like Word for Mac to do any sort of change tracking or markup. CriticMarkup feels like an extension of Markdown in that it allows you, through a simple and easily understandable syntax, to insert additions, deletions, substitutions, comments, and highlights into plain text.