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Ear-Training / Fundamentals

Robert Whelan and David Crane have created a collection of drills that anyone with a Java-enabled browser can use online. Right now there are modules for clef-reading, intervals, scales, and chords. Most online activities I've looked at are useless, hideous contraptions, but this site is the brilliant exception to the rule. My one caveat is that you should probably tweak the settings of each exercise before you start, so that you begin with a manageable task and then expand.
This is a nerdy piece of software for Windows and Linux that can drill intervals, chords, rhythms, even simple melodic dictation.
I have also made a text-based rudiments program, and two ear-training programs, Singing Cells and Interval Blaster.

Atonal Theory Tools

A neat-looking set-class calculator with a broad assortment of functions. This latest version can even take input from a MIDI keyboard.
A command-line program for exploring pc sets. Gives very detailed info on the properties of a set, with options to explore subsets, supersets, combination, similarity and transformations. Among the programs in a similar format (mod12, AthenaCL) I'd recommend starting here. The program includes some terse documentation, and one could presumably learn much more about its output from Buchler's dissertation tool that explores sets of pitches (as opposed to pitch-classes.)
Ariza seems to have started with a command-line utility for making his own algorhythmic compositions, but then he packed it with all kinds of analytic measures. AthenaCL can give lots of set-class information, do similarity measures, and even explore voice-leading possibilities between sets (drawing on recent work by Joseph Straus). Somehow this data can be assembled into a score or even an audio file via CSound. This program is written in the Python language, and is therefore functional on many platforms including PC and Mac. You must install python (at www.python.org) before installing AthenaCL.
mod12 by Thomas Demske
Download mod12-v3.0.zip [193K]. An old MS-DOS program. Worked as a simple set calculator, and had some functions for advanced set research.
And of course there is my own Post-Tonal Ear-Training Suite

Research and Advanced Topics

Fascinating. Can create, examine, and play microtonal scales. It can even adapt existing MIDI files to a microtonal system.
Last updated 7/29/19 by Dave Smey. Please email me with new links, comments, questions.
(Thanks to Michael Buchler for links.)