The following is sourced from my favorite internet lesson page:

Shut Up And Play

Do yourself a big favor and listen to this with a good set of head phones. Sound quality is superb, as are the lessons.

Harmonic Tuning

When you tune to an electronic tuner, you are tuned to the tuner. But a guitar must be tuned to itself for best tone. Here is how this works: With harmonic tuning, you compare a fretted tone to a harmonic tone or a harmonic tone to a harmonic tone on a different string. The frequencies should match. If they don’t, you will hear beat frequencies. That is; you will hear a WA-WA-WA sound. Pitches (string frequencies generated by picking) with matching frequencies produce a steady tone - no warble or WA-WA-WA. You can hear the WA-WA-WA slow as the pitches begin to match as you increase string tension. When comparing tones, start with the fretted string pitch below the harmonic pitch and tune up gradually.

1. First, tune to your electronic tuner or tune as you normally do but leave strings a little below pitch
2. Make sure ’D’ string is at correct pitch.
3. G 7th ⇒ D12H (tune G string at 7th fret to the D string 12th fret harmonic)
4. B 3rd ⇒ D12H
5. E 3rd ⇒ G12H
6. A 5H ⇒ D7H (or A12H ⇒ G 2nd)
7. E 5H ⇒ A7H (or Low E 5H ⇒ High E Open)
8. Start tuning from below the pitch and come up to the pitch. When tuning a guitar with all the harmonics present (like our Harmony rebuilds!) you can hear the dissonant harmonic beat frequencies resolve into a consonant or smooth tone as you bring the string to correct tune. Tune slowly.