Why I went for HTML is the ability to embed images (via data URI). This allows for a note to be a single, standalone file that can easily be shared or moved around without losing track of its images.
Even if you want to open a note in 20 years from now you can do so with a browser (assuming HTML will still be around then). You'll get a fully formatted document. For Markdown you can always use a text editor, but to get formatting and images to show, you'll need a Markdown compatible app.
UPDATE: I gave Zim a try and noticed another difference, file format aside: the app I'm working on will show all files in your folder structure, including PDFs, etc. It renders a preview with QuickLook and allows to open the document with its default app.
This comes in very handy when you want to mix & match notes and other documents. For example, let's say you have a hotel reservation as PDF, you could attach a note with driving directions all in the app.