This is a really interesting question. I had, by most standards, a very productive PhD and will share some advice that helped me. You can PM me or post here if you have specific questions.
I have to start out by saying that there is a huge component of luck involved. It is also very lab and advisor specific. Some fields are more prone to rapid publication of small developments while other fields you just publish one Nature paper with an entire thesis worth of work. Most of this advice applies either way. I'm going to leave out any advice about how to choose an advisor.
I'll also try to focus on very specific advice. Of course you should think about science all the time, put in the hours, read papers, blah blah blah. That advice isn't useful because you already know that.
So:
1) Work on multiple projects at once. You know that down time you have between gels, or while you are waiting for your mice to breed. Work on something else during that time. Get 1 or more side projects. Odds are, after time, your side project will end up being your main project after your main project bombs. At any given time you should be doing 3 or 4 different things.
2) Collaborate with as many people as possible. Once you've been in a lab for 1-2 years, you probably have developed 1 or more skills or some knowledge set that no one else at your institution has. Talk to other people in your department and other departments and think of ways you can apply your skill to their niche. Every conference you go to, think about how it applies to your work. Then start a new side project based on your ideas (see #1 above).
3) Start writing the paper as soon as you start the project. Literally. Sit down and write an outline of what you expect your paper to be. Plan your introduction, write the methods, plan the sections of the results. Prepare a list of what you expect each individual figure to be. Then, start doing the work that you need to obtain that data. I can't overemphasize this. It's so much easier to decide what to do when you've already planned it out. It also makes #4 much easier.
4) Limit your unnecessary experiments. If it doesn't pertain to your plan for your paper (or at least a stepwise way to get toward it), don't do it. If I had a nickle for every time I saw someone do an experiment for a week that they didn't need to do because the results were irrelevant to their final message, I'd be rich. You might as well come in, pour reagents down the drain, and go home.
5) Split huge papers into 2 managable papers. I'm sure someone is going to take exception to this, but whatever. Also, some fields don't tolerate this. However, a paper doesn't need to have 8 figures with 4 panels each. The best papers I ever read have a single, manageable message, that is made simply. I put it down and I can summarize in 1 or 2 sentences what it means. Think about that when you're doing your work.
6) Don't get tripped up by personality conflicts. Navigating grad school is like overseeing negotiations between Israel and Palestine. You need to be freakin Madeleine Albright out there, working both sides. You have to stand up to your advisor, your committee members, and everyone you work with by sheer force of will and bend them in the direction that helps you the most. You need allies other than your advisor, and I recommend you make friends with the biggest heavyweight in your department. Put him/her on your committee, and convince him you are right. Everyone else will fall in line.
7) Be willing to accept publication in a lesser journal, sometimes. Before you run that western blot for the 100th straight time on the off chance that Cell is going to accept your paper, take a realistic look in the mirror and assess your chances. It may be better to get your paper published in a well read specialty journal and just move on to your next thing. If you're in danger of getting scooped especially, maybe just get the paper out there to lay the groundwork for the one that does have a chance. This is a delicate balance, because you want to publish in the best available journals. However, spending a year working on some bull**** to get in a journal that has an impact factor of 9 instead of 6, forget it.
This is only a start, but maybe it will help someone.