First: quarter tones are implemented by emitting the nearest 12-ET note and a quarter-tone pitch bend if applicable, so that for instance cih' (quarter tone sharper than Middle C) is MIDI note 60 (c') with a +50 cent pitch bend. And MIDI pitch bends affect the entire channel; so if there are two notes that require different bend amounts, then they have to be in different MIDI channels.
It's possible to use post-processing to convert the pitch bends into MIDI Tuning Standard messages. These can be understood by Timidity and potentially FluidSynth and hopefully others. More details and scripts here:
http://x31eq.com/lilypond/ Graham
