The Researcher’s Bible: http://homepages.inf.ed.ac.uk/bundy/how-tos/resbible.html
(it contains a lot of useful information: common problems of research students, psychological problems, how to choose a research project, or writing and reading tips)
PhD Grind: http://www.phdgrind.com/ + http://www.youtube.com/watch?v=zHp2rxR2LTc
(a book that describes the full experience of one PhD student in the US)
Useful Apps for Academics: http://libguides.mit.edu/content.php?pid=174869&sid=1481866
A graduate school survival guide: http://www.cs.unc.edu/~azuma/hitch4.html ("Everything I wanted to know about C.S. graduate school at the beginning but didn't learn until later.")
Three stages of PhD: http://xrds.acm.org/article.cfm?aid=2748105
More related to Dutch PhDs, but still relevant: http://science.raphael.poss.name/so-you-want-to-apply-for-a-cs-phd.html
How to do Great Research (Hamming’s You and Your Research lecture): http://www.cs.virginia.edu/~robins/YouAndYourResearch.html + http://www.youtube.com/watch?v=a1zDuOPkMSw
Randy Pausch’s Last Lecture: Really Achieving Your Childhood Dreams: http://www.cmu.edu/randyslecture/
Bret Victor, Inventing on Principle: http://vimeo.com/36579366
This book provides suggestions to both PhD students and their supervisors: http://slpramod.weebly.com/uploads/3/3/2/7/3327933/how_to_get_a_phd.pdf
Some research groups have their own internal workshops or seminars - please update the sections with links to slides or contacts (or any other useful information), so that students from other groups can get in touch and attend the seminar.
On Nov 26 2014, Li-Yi Wei gave a talk “How to make a top research paper while having all the fun”. Some of the advices are on his blog: http://blog.liyiwei.org/?tag=advice, and the slides are (temporarily) under https://www.dropbox.com/s/ontqjhb62qe65x7/siga14.pptx?dl=0
The approach in his talk is in essence: start writing a paper from Day 0 (even if you have just a vague idea), log everything there (including comments -- he uses it instead of email/IM or face-to-face meetings with his students) + use LaTeX (you can easily script/automate things + works better with VCS) + use VCS (Git, SVN, …) for everything.