The core idea is could be described as source code approach to academic writing in which you will need:
- a text editor of your liking for editing the source code
- Notepad is good, but for windows I recommend Markdown Pad and
- for OS X maybe Mou, Clockwork Engine or perhaps TEXTS.
- Also, Sublime Text is an excellent editor of all OS's.
- There are several others if you google
- pandoc for converting source code into formats you like
- latex for scientific journal article pdf's
- in English a this is great starting point: WRITING AND PRESENTING SOCIAL SCIENCE
- in Finnish from my blog: Markdown ja pandoc - tekstipohjaisen tieteellisen kirjoittamisen työvirta
Sublime text 3 in Windows
Gedit 3 in Ubuntu-linux (with embedded shell)
There are several web based solutions and more popping up all the time.
- http://muistio.tieke.fi/
- http://kirjoitusalusta.fi/
- google docs