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Music Fundamentals
This is like a music theory textbook online. It includes great explanations and assignments, although there is not a way to check your completed assignments. It begins with the basics and goes through triads. Midi files are included.
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Ruby Cliff Computing: Learn Guitar Theory With Virtualoso Guitar
This is a fantastic site that teaches basic music reading, especially as related to the guitar. Although the site is a promotional software site, the trial version is excellent by itself.