Producing a thesis (Ph.D, Masters, or undergraduate honours) is a monumental task that can create significant stress. Here I am just going to focus on the mechanics of producing the final document, not the greater challenge of producing the intellectual content.
In most cases there is a deadline, whether imposed by the program, funding running out, or (hopefully) a fixed date to start a job. For many students there is a big rush at the end featuring very long hours, missing "life", neglecting family and sometimes health, exhaustion, anxiety, ...
These problems are compounded if one starts "writing" and producing the thesis document at the very end, with the final deadline looming. Furthermore, this can be much slower and more frustrating if you have to do some of the mechanics (e.g. ordering and numbering references) by hand or at least learn to use software to do it automatically. Compared to 30 years ago, the mechanics is now so much easier because of software that automates many of the tedious tasks such as ordering and numbering.
Let me encourage you to start now on the mechanics.
First, you need to decide on and learn relevant software and start using it every step of the way. Talk to other students (just finished or finishing) and postdocs to find out what they used, and the relative merits.
Here are some concrete issues to consider.
Keeping track of references.
From day one you will start downloading (and hopefully reading) papers. By the end you will (hopefully) have hundreds of references. How are you going to sort them and organise them? If when you start writing you just have hundreds of PDFs in a folder on your computer, life is going to be difficult if you have to start looking at them one by one to find some particular reference you need.
I use the wonderful program Papers. Others like Endnote. The main thing is to find something that works for you, including interfacing smoothly with your word processor program.
Ordering and formatting of references.
For LaTeX, BibTeX does this nicely, provided you learn how to get it to produce the desired format.
Generating a bibliography.
Papers can easily produce a .bib file for BibTex.
Producing graphs and schematics and incorporating figures in the document.
On a previous post, commenters on a post discussed useful freeware for plotting data.
Spell and grammar check.
This is particularly important for students whose English is weak or are dyslexic. Advisors and examiners really get irritated by too many typos. I have never found a decent spell checker for LaTex. Any recommendations?
This should include all the relevant sections from cover page to lists of figures to acknowledgements. It should automatically order and number everything: pages, chapters, figures, tables, equations, references, ....
Keep it simple.
Avoid personalised versions of templates and software (e.g. LaTeX macros), either from you or someone else. My limited experience is that these are often not as portable as hoped/claimed and lead to small bugs that can waste precious time trying to fix.
Backup everything regularly.
This is so easy but it is amazing and disappointing how I still hear of students losing work. Dropbox, cheap portable Terabyte drives, and Time Machine on Mac's make this inexcusable.
Don't just backup the thesis document, but all your data, codes, references, ....
Hard drives do crash and laptops do get lost or stolen...
Practise writing now.
Writing is hard work. Don't wait until the final stages of the thesis to start to learn how to write. It is too late.
Getting feedback from your advisor now.
Again during the final stages is not to learn how she likes things formatted or how to write figure captions.
What software would you recommend or avoid?