MuseScore is a free software music notation editor with playback. Its built-in capabilities are already somewhat friendly to xenharmonic music (it supports many accidental shapes natively, and the tuning of any note can be changed for playback), and it can be made an even more powerful tool with plugins.
The following plugins only affect the playback of the piece - they don't do anything to the appearance of the score. Generally they have a "retune" button that retunes all or part of the piece to pitches computed from the score (so they do not work in real time - you have to retune again after any changes).
- Fifths-based tuning by John Moriarty - as the name implies, you set the size of your "fifth" and then it auto-tunes your score based on that. Uses the MuseScore Tonal Pitch Class (tpc) enum, so it only supports the four "standard" accidentals: flat, sharp, double-flat, and double-sharp (x). Does not allow octave stretch - octaves are always 2/1.
- Porcupine tunings by John Moriarty - you set the size of the porcupine generator, and then it auto-tunes your score based on that. The natural notes are tuned to porcupine. The sharp and flat modify pitches by the chroma from that 7-note MOS scale. Same implementation as Fifths-based tuning above.
- Accidental Tuner by Gilbert Yammine - lets you define the amount by which any given accidental modifies a pitch, then you can retune all or part of the score automatically based on that. The seven naturals cannot be retuned.
- n-EDO retuner plugin by euwbah et al. - lets you set any EDO tuning. Supports microtonal accidentals in alternative symbols for ups and downs notation.