Identification of pitches

I am developing software to automatically implement alternate tunings in
MIDI files through the use of pitch bends or other methods. The idea is to
allow notation on a staff or piano roll without regard to the actual pitches
represented, then processing the resultant MIDI file along with a scale file
to produce a second MIDI file with the notes adjusted and pitch bends
inserted before each note to tune to the proper pitch on-the-fly. Is there
an established system that precisely identifies each pitch? I know that the
MIDI note numbers identify 12TET but what about the rest?

Thanks,
Brian M. Ames
Visit The Ames Hymn Collection
http://junior.apk.net/~bmames
The Ames Classical Collection
http://www.geocities.com/Vienna/Strasse/7398