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.
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.