I always wished Evernote would store my text as text and Alternote seems to be the first tool that (at least tricks me---in the good sense) that I can use Markdown to enter my notes.
You should check out Marxico - http://marxi.co - as that has pretty comprehensive Markdown support.
Full Markdown support is coming in version 2.0 early Spring.
So far it's a much better experience than the Evernote editor. Now if we can only figure out a way to shoehorn in some encryption...
Encrypted text support will be added in one of updates after the Mac App Store release.
Excellent app. Very clean interface. It's like your default note app, but connected with Evernote