First and foremost, you need a reliable and flexible text editor. I personally suggest LaTex or Lyx to everyone. For beginners, it might be a drag but after a little bit you will appreciate the strength and flexibility. Then, you need a very good vector graphics editor, so your image does not get distorted after resizing. There are several open source softwares out there such as Inkscape, XFig, etc. However, it is important to choose something that you are very comfortable with, since creating new images usually take a long time. You also need a flexible software to plot your equations and save as SVG. I suggest to use GNU plot. Finally, yo need an easy-to-use citation manager software such as JabRef, Refworks, or Zotero.
Now that you have all the tools, you need some strategy to start writing your thesis. It is usually suggested to leave the introduction and conclusion chapters to the end. Now, I will outline the strategy I find useful for writing a paper or a thesis. Create a folder for every chapter (or section in the case of paper). Each day that you make some changes to the particular chapter, start with a new copy of the last version of that chapter in a new folder. Name the folder, the day you are working on that chapter. Finally, make a log file (a text file) and write changes you have made at the end of the day. See below figure.
Finally, DO NOT FORGET TO KEEP A BACKUP FROM YOUR CHANGES.