I'm a big fan of the work of Heinrich Schenker. Please see Tom Pankhurst's excellent Schenker site.
More information on Schenker will be posted soon.

If you're interested in counterpoint, I highly recommend the book Counterpoint in Composition . In my opinion, it's by far the best counterpoint book available in English. It's not a beginner's book, though. If you want to start your study of counterpoint at the very beginning, you can't do better than the book that Bach, Haydn, Mozart, and Beethoven all learned from: Johann Joseph Fux's Gradus Ad Parnassum.

Much more information on counterpoint and many other aspects of music theory will appear on this page in due course. In the meantime, you might enjoy the web site of the Texas Institute of Theory. The site itself is now (sadly) defunct, but it lives on in the internet archive.