I wrote my PhD thesis in LaTeX, there are many advantages to this including perfect formatting, PDF links, and rock solid stability. Pretty much everyone I know has had major issues writing a thesis in Microsoft Word. The template below should be of some help in creating a nicely formatted thesis.
LaTeX
I wrote this guide because I had many references in EndNote that I wanted to use in my LaTeX documents. I had to figure all this out the hard way — by lots of trial and error, if you follow this guide it should be easy for you. There are a few points to make: I have used every EndNote version since 4, but when I did my thesis I used version 9. This guide should work for other versions, unless Endnote have drastically changed something.
I am interested in various aspects of computing, some of these are detailed below.
LaTeX
LaTeX is an excellent typesetting system. I used it to write my PhD thesis and other files such as my CV. In writing such a large document like a thesis I learnt a few tricks, and I wrote some of my tips on these pages: Using Endnote with LaTeX and BibTeX and A thesis template for Auckland University