There are some MIDI programs and plugins that will allow "microtuning" of pitches using MIDI. First, info on this, and then a more simple idea to achieve what you want....
Check out
http://www.lucytune.com/ for an interesting look at "true" tuning and intervals based on scale.
This specific page:
http://www.lucytune.com/midi_and_key...itch_bend.html
Has some MIDI tools to apply the "lucy tuning" approach, and most of the same tools could be used to do what you want, I think.
Now for a more simple approach: The first thing that popped into my head thinking about 1/4 tone intervals is how you would go about mapping tones to keys. How about just using
two keyboards, and tune one up (or down) a 1/4 step. That way you still have the familiar tones on one keyboard, and the "in-between" tones on the second keyboard. This would also be much simpler than remapping the entire keyboard to 1/4 tones, in which case you'd be dealing with strange fingerings of chords in very unfamiliar ways.
Also, if you haven't yet discovered it, the Virus has a "Pure" vs. "Tempered" tuning adjustment, which relates more to the Lucy Tuning links rather than your question, but I think it's all interesting!
Blair