Regarding checkboxes, theoretically you could create notes with checkboxes in Egretlist and then move them to whichever notebook you want them in. Not ideal (and not free!) but perhaps a work around?

BTW, since there have been a couple of articles on Markdown at 40tech.com recently, I was wondering if you guys had come across Elements 2.0? It’s an iPhone/iPad app that supports Markdown, Dropbox and Evernote.