It should be easy to read for students, and include discussion of software. This will be used primarily with social sciences (mostly psychology and education) students.
I do recommend "Research Methods for Education ( 2nd edition) by Peter Newby." It doesn't include any sort of software discussion but it, surely, does the job.
http://www.amazon.com/Research-Methods-Education-second-Peter/dp/0273775103
This is a large and free online resource and you can follow the course in MLwiN (a version is free to download) , Stata and and for some parts in SPSS
http://www.bristol.ac.uk/cmm/learning/online-course/
Here are the modules - we have tried to write them into two parts - concepts and then practice (using particular software)
Using quantitative data in research (watch video introduction)
Introduction to quantitative data analysis (watch video introduction)
Multiple regression
Multilevel structures and classifications (watch video introduction)
Introduction to multilevel modelling - This one should meet your needs
Regression models for binary responses
Multilevel models for binary responses
Multilevel modelling in practice: Research questions, data preparation and analysis
Single-level and multilevel models for ordinal responses
Single-level and multilevel models for nominal responses
Three-level multilevel models
Cross-classified multilevel models
Multiple membership multilevel models
Missing Data
Multilevel Modelling of Repeated Measures Data
and it is part of a wider resource for multilevel modelling
http://www.bristol.ac.uk/cmm/software/mlwin/mlwin-resources.html
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