Now that we're listing them:
- The normal matilde tracker has a command called "harmonic play" (17) which lets you multiply the base frequency of the note being played by an integer number, giving you a super easy way to play just intonation.
- There's a special version of matilde tracker that supports finetuning of the 12 semitones in the octave. This approach makes it fairly easy to do arabic/turkish maqam compatible tunings.
- Roland JV1080 (a hardware synth) supports finetuning of the 12 semitones in the octave.