Three Tools. One System.
This is the place where all your notes come together and build a critical mass of ideas. Developed by Daniel Lüdecke to emulate and improve Luhmann’s famous slip-box. This presentation is a good introduction.
The Reference Manager
This is the place to store all your references and articles. Zotero has some really neat features that makes your life much easier. As an open-source project, it is constantly improved.
This is where the actual writing is done. Any editor would do it, but if I had to decide, I would recommend LibreOffice.
As another open-source project, this program is also improving constantly.