Here are a few sites that may come in handy when trying to learn new areas of music theory. Feel free to contribute your own via PM or posting below!
General Theory
Lessons on Musictheory.net - General introductory lessons to the principles of music theory
Overview of all Scales and Modes (FR, use translate) - Comprehensive overview of how to form pretty much every scale possible under 12-tone Equal Temperament.
The Eye that Hears, the Ear that Sees - Very good more advanced overview of harmonic concepts in traditional theory (in both English and French) - it's a bit of a slog in the English translation, but some great points and tons of examples.
Euler's Music Theory - For all of you obsessive math nerds out there, the guy even had time to develop his own theory on music!
Orchestration
Garritan Interactive Rimsky-Korsakov Principles of Orchestration - A nice read for a rainy day, a mostly-complete orchestration manual with good tips!
Rimsky-Korsakov; full text - Full text version of the previous, but with no audio examples or commentary. Good for expanding upon the above link when done.
Philharmonia Orchestra Guide to Instruments - General overview of the different kinds of instruments in the orchestra with videos.
Indiana (ISU) Guide to Instruments - More structured walkthrough of the various kinds of instruments with recorded examples of many articulations.
Vienna Academy: Instrumentology - Another walkthrough of the various kinds of instruments with recorded examples of many articulations and historical contexts.
Orchestration Online - Great (perhaps slightly overly-assertive) videos discussing orchestration, composing, books on the previous, time management, and more by professional orchestrator/composer Thomas Goss.
deBreve - Anther perhaps slightly overly-assertive take on some orchestration concepts and topics.
Temperaments, Tuning
Rollingball's Temperaments Visualized site - Great introduction and overview of many historical temperaments, with links out to other sites about temperaments worth checking out!
Evolution of High Pitch and Low Pitch - Useful article for anyone into Pre-1930's brass instruments or brass band music (Civil War, Sousa, etc.).
Why 432 is a Myth - The most complete, researched, and fact-driven rebuttal to the 432 hysteria to date. I carry this around instead of pepper-spray.
Acoustics (as an aside)
Intro to Musical Acoustics - The Aussies know how it works, so you should too!
Acoustics of Bells - Short overview of the history and acoustics of bells (should you want to synthesize some)
General Theory
Lessons on Musictheory.net - General introductory lessons to the principles of music theory
Overview of all Scales and Modes (FR, use translate) - Comprehensive overview of how to form pretty much every scale possible under 12-tone Equal Temperament.
The Eye that Hears, the Ear that Sees - Very good more advanced overview of harmonic concepts in traditional theory (in both English and French) - it's a bit of a slog in the English translation, but some great points and tons of examples.
Euler's Music Theory - For all of you obsessive math nerds out there, the guy even had time to develop his own theory on music!
Orchestration
Garritan Interactive Rimsky-Korsakov Principles of Orchestration - A nice read for a rainy day, a mostly-complete orchestration manual with good tips!
Rimsky-Korsakov; full text - Full text version of the previous, but with no audio examples or commentary. Good for expanding upon the above link when done.
Philharmonia Orchestra Guide to Instruments - General overview of the different kinds of instruments in the orchestra with videos.
Indiana (ISU) Guide to Instruments - More structured walkthrough of the various kinds of instruments with recorded examples of many articulations.
Vienna Academy: Instrumentology - Another walkthrough of the various kinds of instruments with recorded examples of many articulations and historical contexts.
Orchestration Online - Great (perhaps slightly overly-assertive) videos discussing orchestration, composing, books on the previous, time management, and more by professional orchestrator/composer Thomas Goss.
deBreve - Anther perhaps slightly overly-assertive take on some orchestration concepts and topics.
Temperaments, Tuning
Rollingball's Temperaments Visualized site - Great introduction and overview of many historical temperaments, with links out to other sites about temperaments worth checking out!
Evolution of High Pitch and Low Pitch - Useful article for anyone into Pre-1930's brass instruments or brass band music (Civil War, Sousa, etc.).
Why 432 is a Myth - The most complete, researched, and fact-driven rebuttal to the 432 hysteria to date. I carry this around instead of pepper-spray.
Acoustics (as an aside)
Intro to Musical Acoustics - The Aussies know how it works, so you should too!
Acoustics of Bells - Short overview of the history and acoustics of bells (should you want to synthesize some)
Sample library developer, composer, and amateur organologist at Versilian Studios.