I second the Robert Yin, Case Study Research (currently into its 4th edition). It is a real classic and seems to be cited by just about every second person-which is how I came to buy it.
For students who are not yet into their Phd but want helpful texts for structuring Master's theses then How to Write a Master's Thesis by Yvonne N Bui is really really useful. (However, I am recommending this for your Master's students only obviously). The Bui one isn't just research methods it is a thorough overall 'how to' book and it makes for a great substitute supervisor, when your own is some where else or otherwise unavailable! It basically tells you how to plan, write and present your research really methodically, step by step.
There is this really interesting (slightly alternative) book by Marilyn Lichtman on Qualitative Research in Education and of course the standard Creswell's Educational Research. These are focused on research in Education (obviously:)!) but they still go into methodologies really well. The Creswell one provides models or samples as does Yin and Bui. The Lichtman one seems a bit too alternative at times but she goes into the ethics and issues of conducting qualitative research very thoroughly and if you are working with people, then it can be really useful at times.