RhythmTutor - [Win-Mac] Music instruction software: learn to sight-read musical rhythm notation. Demo available.
Rising Software - Offers Auralia, an ear training program for Win and Mac and Musition, a theory training program for Win.
Scala - Experiment with musical tunings: equal and historical temperaments, just intonation, microtonal and non-Western scales. Win, Linux, OSX.
Tete - Open-source ear-training software. Recognise the relationships between notes of different pitches. Play and be tested on intervals, chords, and scales.
Treblis Software Corp - Music theory and appreciation software for intermediate, high school, and college level students and their instructors.