The Control Lectures series by Brian Douglas on YouTube is a fantastic resource (https://www.youtube.com/user/ControlLectures). Also U. Mich. has a great set of control tutorials put together with a focus on implementations in MATLAB/Simulink (http://ctms.engin.umich.edu/CTMS).

All of my own experience in controls (both as a student and professional) uses MATLAB/Simulink to model and generate controller code. Other tools are out there, but I don't know much about them.