I'm pulling the following from a
blog comment I wrote a while ago on another site, so forgive me if it seems a little inconsistent or dumbed down at times. It contains a whole bunch of resources and courses that are available online, as well as links to some very helpful theory books.
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Basic Theory
Yale lecture series to start you off
How to Listen to and Understand Great Music, by Robert Greenberg
Understanding the fundamentals of music, by Robert Greenberg
More advanced broad stuff
More Robert Greenberg lectures - From these you will learn how to analyse and critically listen to music, you will become familiar with the major works of composers you choose to study, and you will learn a lot of important music history. Greenberg is a fantastic teacher. I'd highly recommend his "30 greatest orchestral works" to start out with.
Leonard Bernstein's Young Peoples concerts - Old, but absolutely fantastic. Bernstein was a GREAT teacher.
Leonard Bernstein's Omnibus series - Even OLDER, but even more fantastic. Definitely check out the
one about Beethoven's fifth symphony, in which he takes Beethoven's discarded sketches for the work and suggests why he discarded them
Leonard Bernstein's Harvard Lecture Series - More Leonard Bernstein. In this, he makes a very detailed comparison of music to linguistics and literature. It includes a MINDBLOWING explanation of harmony and includes very detailed analyses of certain aspects of
Mozart's 40th symphony and
Beethoven's 6th symphony.
Harmony
Aldwell and Schacter's "Harmony and Voice Leading" - This is the standard college book on harmony these days.
Tchaikovsky's book on harmony - This one, while a little old (written in the 1880s) is VERY clear and to the point. I'd recommend this for starting out on.
Arnold Schoenberg's books on harmony and composition in general - I've only linked to one, but the others aren't too difficult to find.
Counterpoint
Counterpoint uses the "rules" of harmony and puts them into the context of writing melodies. Counterpoint will teach you how to write two or more melodies at the same time convincingly. In my opinion, it's far more important than harmony. It's a very boring and monotonous subject, but it's SO worth the effort of studying it.
Counterpoint in Composition, by Felix Salzer - An excellent book that not only teaches you the theory, but also shows you examples of how the masters interpreted and used it, which in my opinion, textbooks should do far more often.
Johann Joseph Fux's Gradus ad Parnassum - This is VERY old (1720s), so the language in it will be very weird and contain many unnecessary refrences to God. Don't let that put you off though, in its day, this book was praised by Bach and Handel. A few years later, a man named Leopold Mozart taught counterpoint to his son from its pages. Joseph Haydn religiously studied from this book, followed by Beethoven, followed by Schubert, Chopin, Brahms, Berlioz... need I go on?
Form
You may or may not find the subject of form relevant to you, but I ask you to seriously consider reading a book called
Classical Form by William Caplin. It completely turned my understanding of music upside down and made me listen to everything in a whole new way. I cannot recommend it enough. Even if you end up never using the forms he talks about in such detail, it's worth knowing them.
Orchestration
If you plan to start writing for orchestra, this is a must.
Samuel Adler's "Orchestration" - An excellent book that comes with a CD with MANY audio and video examples of what he's talking about. This is an invaluable resource.
Thomas Goss' OrchestrationOnline Youtube channel - Tom is a professional orchestrator whom I have much respect for. He's done some fantastic videos discussing the subject of Orchestration.