Editor or notes application with Markdown support?

nvALT does the trick. I prefer the plain Notational Velocity myself, but Markdown fans seem to really like the nvALT fork.

Mou

Mou is my favourite Markdown editor for editing GitHub files and other documentation. Its live preview is priceless for editing in this way, especially using the specifically-designed GitHub theme that mimics the end result as shown on GitHub's preview and wiki pages.

The app also lets you export to HTML along with the CSS so that you can upload the documentation outside of GitHub but retain the style.

The app is one of a very few apps that even supports tables not in the core Markdown:

Mou can be launched from the command line with a file using the standard OS X app launching method:

open -a Mou text.md

It's not a note taker per se, but Textmate has a Markdown mode that will make it easier to use some of the syntax. Like bold, italic, list, etc.