I came up with my "ultimate method" after reading that cheap Dover book on Piano Tuning. I believe it is the most direct and accurate way possible (so please school me if I err!).

 * Start with a reliable A 440. I use a tuning fork.
 * Tune the 1/4 (5th fret) harmonic of the A string in unison with the A 440.
 * Tune the D to a perfect fourth above the A. (You can use the 2/3 (7th fret) harmonic if you like.)
 * Nudge the D ever-so-slightly *sharp*, until you hear a *very slow* beat (about 3 beats over 5 seconds.
 * Tune the G from the D in the same way (just a smidgen sharp).
 * Tune the low E from the A in a contrariwise manner: scoop in from the D# side until you find the slow beat just before a perfect fourth.
 * Tune the High E from the low E. (You can use the 1/4 (fifth fret) harmonic if you like.)
 * Tune the B from the E the same way you took the low E from the A: scoop in from the A# side until you hear the slow beat.

And finally, check your work with the open triads: D-G-B and G-B-E. They should sound balanced and distinct. You can hear all three notes, but none of them sting. If the triads don't sound good, nothing else will either: Do it again *in exactly the same sequence.* You can also check all the tempered fourths against each other. They should all sound like identical intervals.

It is *very difficult* to hear the beats. One trick I've found is to hold my right hand a few inches over the guitar as I sound the notes. I seem to be able to "feel" the beats more easily than I can hear them.

Tempered fourths gives you equal temperament. But for music that stays in a diatonic key, you can make a few slight adjustments. Starting from equal temperament, fret the root chord of the key.  Then nudge the fifth up a smidgen (to shake off the temper), and scoop the third in a little flatter (a Helmholtz third). Remember which strings you altered so you can scoop them back into tempered from the "stationary" strings.