Update: Since this post was first written, some of the course offerings have changed. The course described below is still available for free, but you may want to use another platform, such as edX. See this page for the most updated listings.
I absolutely love the music theory and history courses offered by The Berklee School of Music. It offers a six week course called Developing Your Musicianship that was originally designed for incoming freshmen that have no music theory background. It is great for high school students to take before taking AP Music Theory or before they start college. The course has a specific focus on harmony and ear training: two topics that are often overlooked. From the website:
The instructor videos are engaging and fun. The handouts are really useful and well-done. There are quizzes given along the way that check for understanding. If you have a student who is committed to learning theory, this is the course for him/her (or you if you need to brush up!). It is only offered during certain weeks of the year though, so you have to plan ahead.