Extensions to other kinds of classes
The methods described here were originally developed for large, freshman or sophomore level science classes that were traditionally delivered by lecture.  But, that does not exclude the possibility to extended them to any class, in any discipline.  To date, we have done this in more than eight different engineering classes at the College of Engineering at the University of Michigan.  The first class was the introductory materials course described on this website. We have also converted a graduate level electron microscopy class, a graduate image processing class, a graduate microelectronics manufacturing course, a quantitative cell biology course for seniors, environmental and water resources course for seniors, the lecture component of the biomedical engineering capstone design course, and in a material science and engineering class on the structure of materials.  
Class size ranged from 20 and 90 students.  All classes replaced lecture entirely by using team-based active learning techniques during class time. Whiteboards were used in all all of these classes. Seven of the eight classes used reading annotation as the first introduction to the material.  All classes used formative assessment and feedback techniques for homework and readiness assurance activities.  Yet, different courses approached the details quite differently.  For example, the graduate image processing course traditionally used take home exams.  These would simply not work using a computer graded in class RAA.  So they gave the same take-home exam as usual where the students were told to work independently, and then bring their work to class. Then they did a group test activity (similar to the group homework activity) to make sure they could all eventually solve every problem on the exam with the help of each other and the instructional staff.  Then, just like in the regular RAA process, they were given a grade for their individual effort, measured for accuracy (unlike the homework activity), and their group effort. These two grades were then averaged together for each student's grade.  
Other classes required that students annotate short videos for the first introduction of the material. One of the nice features of nb.mit.edu is that a student can watch a video and make annotations to the timeline in the video and have a discussion.  So, it is relatively easy to find different ways to approach different classes with a little creativity and flexibility.