Janet Stemwedel's blog article "The price of calling out misconduct" about an article in Science describing the situation of some graduate students who blew the whistle on their advisor is very depressing.
Here we have courageous grad students working to better science by letting the community know that their advisor is making up data, and they end up paying the bill. Janet quotes a fascinating paper from Science and Engineering Ethics by C. K. Gunsalus's excellent paper "How to Blow the Whistle and Still Have a Career Afterwards." I think I will print out a copy for my administration, as the next article is on how to avoid whistleblowing problems in your institution.
Very important is finding both sides to an issue, as many people often misunderstand what is actually happening and start threatening lawsuits without being sure. On the other hand, if it really is misconduct, then you have to do something.