The second half of this free course is now out. The best part of the course, to me (I'm the instructor), is there's a nice long section on shader programming. Exercises include making a toon shader and an anisotropic material shader. I'm also happy with the animation section, as it gives some good grounding and code samples for using keyframing, quaternions, and other elements of three.js that are not well-documented.
What I like about this course's structure is that you can jump around, depending on your interests. Unlike many online courses, you can start this one anytime and take it at your own pace. There's nothing forcing you to do the lessons in order, and each individual video is just a few minutes long so it's easy to go learn just what you want to know. All the videos, code, and course scripts are downloadable - the course scripts alone add up to 850 pages.