LaTeX +1.
Use your first year to gain some skills (including writing in LaTeX!). Learn a new programming language if relevant (find out what is status quo in your field), brush up on your maths if needed. Don’t forget it’s as much about acquiring a skill set as getting the title, and you will never have such a rich opportunity to acquire random talents.
I’ll stick my neck out and say if you’re working in science then learning to use a Linux system is a solid step to take, though I guess some will disagree. You will find post doc positions in many fields that demand linux experience though.
Mind mapping software can be good for getting your ideas together.
Accept that some supervisors are crap, and need managing – try to find out early on (from their other PhDs) if yours is one of them.
Read PhD comics. here