I started to use markdown to take notes.
I use marked to view my markdown notes and its beautiful.
But as my notes get longer I find it diff
Depending on your workflow, you might want to look at strapdown
That's a fork of the original one (http://strapdownjs.com) that adds the generation of the table of content.
There's an apache config file on the repo (might not be properly updated yet) to wrap plain markdown on the fly, if you prefer not writing in html files.