You have finished all the experiments and are in the middle of writing that wonderful manuscript that will change not only the field you are working in but also your personal career. But then you encounter all these complicated issues related to paper writing, including duplicate publications, joint first authors, multi-authored papers and paper rejections.
You understand that these are sensitive ethical issues and you want to do the right thing. When is joint first authorship a problem, can I publish a paper a second time if it is written in another language, should my department head be a coauthor, etc. You will of course discuss these questions with your coauthors, but where else can you look for advice?
Journal author guidelines. The first and most useful place to look for advice, both for technical aspects, but also for ethical issues surrounding your manuscript. Author guidelines probably often are read too late (days before submission) and not carefully enough. The Editorial policies of Nature are found here.
ICMJE (International Commitee of Medical Journal Editors). The Uniform Requirements for Manuscripts Submitted to Biomedical Journals could be the next place for advice. The text contains a lot of useful information for both authors and editors, including special reporting guidelines such as CONSORT for randomized controlled trials.
COPE (Committee on Publication Ethics) COPE is another useful resource that I recently discovered. I especially like the Case section, where real-life examples such as ghost authorship or reviewer competing interests are discussed.
If there are still open questions after reading these guidelines, join the regular discussion in the Nature Network blogs and forums on these topics, most recently Nobel prize-winning lab retracts paper from Nature in the Neuroscience forum.