Teoría: Music Theory Web
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.
Understanding Basic Music Theory
A free online course on the fundamentals of music theory
MusicTheory.Net
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.
Peter Schubert Videos
Musicologist Peter Schubert has uploaded videos discussing and demonstrating live improvising and improvisation of a canon.
Musicards
Online flashcards for music theory. Includes flashcards for reading the tenor and alto clefs.
Musicca
Online exercises and learning tools in foundational music theory, music notation, and ear training.
Dolmetsch Foundation's Music Theory and History Online
While not precisely an encyclopedia, this is a very rich source of information for the basics of notation, meter and rhythm, chord structures, and so on. The Dolmetsch Foundation is based in England, and so their dictionary is helpful for understanding English or European notational and vocabulary conventions that are different from American music theory conventions.
A Musical Playground
A collection of links that cover the basics of reading common-practice musical notation.