Good records are the foundation stone upon which your research is built. Keep your lab book detailed and accurate, and maintain good records of your samples. See here and here.
Keep an electronic journal.
Five minutes spent writing a bullet point summary of the work you have done each day will build up into an invaluable record. From it you can look back on your thought processes on a given experiment or pick up small, useful pieces of information that would otherwise have been lost in the ether.
Write yourself monthly progress reports.
I would say this the most useful habit you can get yourself into. At the end of each month, you are in a much better position to accurately summarize and reflect on your work during that month than you will be at the end of your studies. A series of well-written monthly reports will build into an easily accessible but detailed account of your work and ease the thesis writing process greatly.
Get into the habit of reading every day
Whether you chose to read one research paper or spend an hour reading every day, over the course of your studies this will build up into a significant amount and contribute massively to your knowledge and abilities, allowing you to become a world expert.
Start writing as early as possible
Even though you will be unsure of exactly what your thesis is finally going to contain you should begin writing what you can, as early as you can. The bulk of the introduction and methods sections can, and should, be written fairly early as a lot of the information included in them is unlikely to change. For writing the main chapters you can begin early on with an outline of chapter titles, with bullet points of likely topics to be included. Over time this skeleton can be built on with work as it is done. This is useful even if a chapter is not complete since writing a chapter from a rough or incomplete outline is easier than starting from scratch.
Read other people?s theses!
Amazingly, I did not actually read a PhD thesis until I was well into writing my own. This was a big mistake and one I would advise you not to make.