Music Visualizer: A Music Comprehension / Music Analysis Tool: Interactively play and display MIDI files with tools to see chords and keys to aid comprehension of tonal aspects of the music, with optional overlaid pitch feedback for learning to sing along with the melody, or in harmony, and several other features.
Recently added: some Ear-Training features for pitch recognition within a key, and sing-along, that are more flexible than the other software I've seen. (It lets you adjust to a random key, random instrument, or change trial notes exactly when you want to and need to for best learning. It lets you play key identification sounds such as scales and tonic cadences exactly when you want them and need them. Sing-along pitch feedback can always be on -- just don't look at it when you don't need it but look at it when it will help you learn.)
Click here for Norm's Music Visualizer Information and/or Download.
Tonegen: A versatile tone generator, including multiple notes, and variable overtone frequencies and volumes, for exploring the science of timbre, "musicality" of sound, consonance, dissonance, roughness (theories of Helmholtz, Terhardt, Parncutt, etc.). Supports rapid switching between up to 3 variants of similar or related sounds (e.g. "probe tones"). Also has separate functionality for testing pitch-discrimination perception, effect of phase-difference between ears, etc. Also, you can take peaks at a point in time from a SpectratunePlus spectrum, and pass them to ToneGen via a clipboard, and you get the same sound, and you can also monkey around with them--shift individual overtone frequencies and intensities.
(One fun thing you can do, is take a musical sound, and switch off and then any overtone. For louder overtones, you get, at least for my ears, a robust "hearing out" of the overtone switched on and off. That is, the sound, once perceptually part of the composite sound with its timbre, stands out as a very engineeringish, non-musical sine. The "hearing out of individual overtone sines" is much studied in the psychoacoustics literature, and some people can learn to do it without turning off and on, or any other manipulation, of the overtone(s) they hear out.)
Click here for TonGen Info.
SpectratunePlus: Does spectral/harmonic analysis on live sound, and also recorded sound. Several aural-feedback, and key/chord-related, features.
Click here for SpectratunePlus Info.
Spectratune An earlier version of SpectratunePlus, limited to analysis of live sounds. Some with live-sound-analysis needs may prefer it, because it has a simpler interface than SpectratunePlus.
Click here for Spectratune Info.
My (now ancient) Spiral Spectrogram Videos (here). These are a video version of the spirals that you get in live mode of SpectratunePlus, recorded against mostly classical music recordings. There is even a full length video of Brahms' German Requiem.