Your suggestion for dealing with the harmonics is great.  But my tuner
attempts to determine by itself which string is being tuned.  I suppose
with expensive programmable filters you could detect the pitch, then dial
in the filter real quick to protect against the harmonics, which
intensify with time.  But if you put in a filter sufficient to chop the
harmonics of the low E string (86 Hz or so) you'd never pick up the high
E two octaves up.

My hackbuddy and I have decided to return to this project and see if we
can get it to work.  The idea will be: count on the fundamental being
strong for the first several cycles (seems to be safe), then start
ignoring any transitions that aren't close to the expected timings.  For
example, if you're tuning the 110 Hz A string, you'd initially get a 110
cycle square wave.  Then as the vibrations decay, you'd start seening
double, triple, or some oddball combination.  If I remember right, the
second harmonic is the most prominent and can be isolated.  But I'll have
to look again.  Anyway, it might be as simple as ignoring every odd
pulse, once the expected pitch is established.  Owell I'll try it and
post the results!

ps: about the code I've offered to put up... I was going to make it
available via ftp this morning but I forgot to move the files.  I'll do
it tomorrow when I'm dialed in from home.

David
--
Their address sums up their attitude: One Microsoft Way
        http://www.rt66.com/dthomas/