Most of these sites use the traditional Roman numeral system of talking about harmonies.
Chordmaps
--One of the very few websites that emphasizes learning the seven harmonies first (the six important ones, actually)
before focusing on the details of scales, intervals, etc.
eMusicTheory.com
--Online theory lessons and interactive exercises
Music Learning Workshop.com
--The same ideas as ours, stated slightly differently and slowly. Very useful.
The Tonal Center
--A mostly conventional explanation of harmony.
TheoryLessons.com
--Online music theory lessons for guitar players.
American Music conference
--Promoting the benefits of music education in society
ReverbLessons.com
--Find local teachers for piano, guitar, strings, voice, songwriting
25 men of classical music
--All about 25 of the best-known classical composers and their works (no women in this list)
The Seven Colors of Music
--A book in website form about the special power of highly-inspired music