Joplin is a free, open source note taking and to-do application. The notes are searchable, can be copied, tagged and modified either from the applications directly or from your own text editor. The notes are in Markdown format.
Hey hunters ! I recently switch from a bunch of Markdown files to... a bunch of organized, sync-ed, open-source powered Markdown files. So far this is one of the best note-taking app I've tested.