I'm a huge fan of markdown. So for that reason, all my notes are kept in that form unless I'm writing them in a book. I also use markdown just about everywhere else (Markdown New Tab plugin, etc).

A couple of features that I've seen in some but definitely not all editors is auto-TOC, and the ability to collapse paragraphs.

What I would pay for: A set of apps, like Todo and Sticky Notes and a Notepad that maintain a shared directory or database so I can use Search and find data that could be anywhere among those different note-taking scenarios. And Todo should be able to link to markdown documents within the app set, etc.