Max

Well, it's well-known for its MIDI capabilities so it might be a good
program to use for pitch-bend microtuning but there are at least two other
ways to use it that might be of interest.
First, it can be used to "drive" or create input for another program. With
Csound, for instance. As it has many interface objects and can build
standalones, it can be used as a front-end for another program. Well, not
with Csound (Cecilia might be a better solution) but with other music
programs that accept either MIDI or text input.
The other possibility is audio. Of course, it might not be as strong an
audio program as, say, Csound or ProTools but Max with MSP (available on
Cycling74) could be used for microtonal music in this way.