Currently I am starting my master thesis, and a tool that I am trying is called Latex.
After googling for a while, tonnes of tools and tutorials came up. In my opinion, Latex is super easy and convenient. I especially like its philosophy “Concentrate on Content not on Layout.” It is so convincing that when we are doing our research or write our document we should concentrate on its content instead of its layout. Architect normally spend too much time of making things pretty instead of making them useful(or making them work).
At the end, I decided to choose my favourite editing tool Aquamacs, the Emacs for the mac, to write it, because it is already integrated with LaTex and its extensions AUCTeX, preview-latex and flyspell.
I also recommend everyone who interested in these tools to try this thesis template as well. Masters/Doctoral Thesis which is super elegant and convenient.
Here is my screenshot of using LaTex in Aquamacs: