Music theory reference, tutorials, exercises, and articles. This site is run by a professor at the Conservatory of Music of Puerto Rico; the site is available in both English and Spanish.
A free online course on the fundamentals of music theory
Ricci Adams's MusicTheory.net has a number of free tools for learning basic music theory, including customizable ear training sessions, elementary notation, rhythm and meter, and key signatures. Matrix calculators (12-tone) and a staff paper generator are also included. A very handy website for the music theory student.
Musicologist Peter Schubert has uploaded videos discussing and demonstrating live improvising and improvisation of a canon.
Peter Schubert and Julie Cumming's video series on Renaissance improvisation practice
Online flashcards for music theory. Includes flashcards for reading the tenor and alto clefs.
Online exercises and learning tools in foundational music theory, music notation, and ear training.