For our startup I have been using github wiki to keep the product specs, design docs, user stories, etc organized and up-to-date. The nice thing about github is you can clone the wiki and work on it locally and push changes up to the server. See this writeup for more info. This is handy because you can then work on the wiki using markdown syntax in a regular text editor versus a web page editor.
The ease of this made me wonder if there was a way to do my normal note taking, code journalling, etc in markdown vs Evernote. I did some looking around and found nvALT, which is a markdown based notebook that can save notes as flat .md files.
So as an experiment I cloned my personal notes wiki from github. After configuring nvALT to use the cloned wiki directory as its directory I could immediately see and search all of my wiki files as nvALT note files. Also I could add new files and they would now become linkable as wiki files. So basically nvALT acts as a note taking system, but notes can be also linked together via a mmd link notation that is supported by the github wiki. You can install the gollum gem and interact with the wiki locally to test the wiki pages.
So I can now create, edit, search notes in markdown, but also link them, as well as view them as a wiki.
I will post again after a few weeks trying out the solution with more info on how it is working.