Here are some guidelines and documents on the supervision of PhD students and on the writing of scientific papers (and not only for PhD students I presume...). I plan to complete this list when time permits, any suggestion of additional material is welcome ! :
"How to guide " a very complete set of documents by Alan Bundy, University of Edinburgh, from the choice of a PhD subject to the structure and content of scientifc papers.
"How to choose a PhD " a nice powerpoint set of recommendations by Serge Abiteboul, INRIA.
"Author and reviewer tutorials" from Springer.
"Tips for writing scientific papers " by Jennifer Widom, IBM, a general resource for academic writers available at the University of Manchester, and a IEEE series of video tutorials on how to write and citing sources.
Last but not least..."how to review papers ", guide and examples suggested by the Conference on Human Factors in Computing Systems (CHI 2005) and a IEEE video explaining the the life cycle of a journal paper during its publication process.
To finish with, I would like to recommend the most acclamed "PhD comics " written by Jorge Cham, inspiring and enjoyable material.