The frequent advice I have been given since I first talk about start a Phd program was: get a notebook and write frequently your notes. Everybody was warning me about the frustration that is when you loose track of some citation or important piece of information...
I also was encouraged to use software to maintain my bibliographical sources and to start writing with Latex the soonest possible.
In my writing course I got to know a couple of new methods for taking notes, and got particularly fond of the Cornell Method. I also use a lot the mapping and the charting method.
However what I have noticed that really helps me to stay focused is writing. That is why I am keeping a journal and I write everything that comes to my mind (trash thoughts included), so I will not waist time remembering that stupid idea I had the other day that might be helpful today...
And here goes a link. This page has great resources about taking effective notes (from the Study Counsel Bureau of Harvard): http://bsc.harvard.edu/onlineresources.htm#notemaking
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