Sites offering music theory, both specific and general, are listed here. Music theory is "a branch of study that includes many different methods for analyzing, classifying, and composing music and the elements of music." (You will find a good writeup of music theory at http://en.wikipedia.org/wiki/Music_theory ) Music Theory is not Musicology. Musicology seeks answers questions for Who, What, Where, When and Why questions. Music Theory seeks answers for How.
Sites offering music theory, both specific and general, are listed here.

Music theory is "a branch of study that includes many different methods for analyzing, classifying, and composing music and the elements of music." "Music theory generally attempts to reduce the practice of composing and playing into rules and ideas."

For music theory journals, magazines, and e-zines.
Lists sites about people who made significant headway in the understanding of musical theory.
Sites which deal with tuning systems (historical and modern), just intonation, and theories of tuning, temperament, and harmelodics. In Baroque times the primary musical "experiments" were not really in melody, rhythm, or harmony, but in instrument building and tuning systems. Likewise, today the things which separate ambient music artists such as Tricky from experimental artists such as the Deep Listening Band or Harry Partch are in the depth to which experimental artists test new tuning systems.