I teach a course entitled "Physics for Audio Engineering Technology", which is essentially an applied acoustics class. In terms of technical difficulty, it's pitched somewhat more advanced than a typical "physics of music" class, but not as technical as a full acoustics class (e.g., we use no differential equations).
I have not yet used these in a course, however many of the wave-related animations (e.g. "Superposition" and "Wave3D" in the Java 1.1 Physlets) look like they would be useful for students as they try to gain an intuitive grasp of these concepts.
The Wave Play applet is useful for teaching students about superposition. Dr. Knop has used it for in-class exercises while teaching PHY1140: Intro to Physics, a prerequisite for Physics for Audio Engineering.