Step1
Turn on your tuner. Have it make an A tone, set at 440Hz. This should match an A4 on an in-tune piano (if A0 is the lowest A on a piano, A4 is 4 octaves up). You can tune your guitar to the piano; however, a piano overpowers the guitar, which is why a tuner is the better choice.
Step2
Play the 5th fret harmonic on your A string. (It is commonly thought among beginning guitarists that the fundamental, the open or fretted note, is what you tune. This is not true. The fundamental is imprecise, containing many other overtones. Your harmonics are much better to tune with. If you don't know what this is, you play the harmonic by barely touching the string in the place you would normally fret. This produces a thin, ringing note. Your 5th fret is 2 octaves above your fundamental, and is one of the overtones that makes up your fundamental. You want to match this harmonic to your A pitch. You can use the tuner aspect of your tuner (the LED's that are red if the note is sharp or flat, or green if the note is in tune) to make sure. Eventually you'll get it right every time.
Step3
Put down the tuner. You only need to find 1 note with the tuner. Most classical guitarists tune with this in mind. Make your low E's 5th fret harmonic. Quickly afterwards (but not too quickly) make the A string's 7th fret harmonic. Tune your low E string so that they match. Your 7th fret harmonic makes a note that is a 4th below the 5th fret harmonic (or the 5th 1 octave up).
Step4
Play the low E 12th fret harmonic. The 12th fret is 1 octave above the open note. Match this to the fretted fundamental note on the A string 7th fret.
Step5
Play the A string 5th fret harmonic again. Match this to your D string 7th fret harmonic.
Step6
Play the A string 12th fret harmonic. Match this to your D string 7th fret fundamental.
Step7
Once you think this is tune, you can check it with one more step that I stumbled across one day. Play your low E 12th fret harmonic. Match this to the E fundamental on your D string (fret and play the second fret). If they are in tune, without a doubt, your bottom 3 notes are in tune.
Step8
Play the D string 5th fret harmonic, match to the G string 7th fret harmonic.
Step9
Play the D string 12th fret harmonic, match to the G string 7th fret fundamental.
Step10
Play the A string 12th fret harmonic, match to the G string 2nd fret fundamental.
Step11
Because of that weird 3rd between your G and B strings, you'll have to change things up a little. Play your G string 9th, or 4th fret harmonic. These are somehow the same notes. These are a little harder to bring out than 5th or 7th and definitely 12th, but try for it anyway. The G string 4th or 9th fret harmonic should match the B string 5th harmonic. If you can't get that 4th or 9th fret harmonic, you can go straight to next step.
Step12
Play the G string 12th fret harmonic. Match to the B string 8th fret fundamental.
Step13
Play the D string 12th fret harmonic. Match to the B string 3rd fret fundamental.
Step14
Play the B string 5th fret harmonic. Match to the high E 7th fret harmonic.
Step15
Play the B string 12th fret harmonic. Match to the high E 7th fret fundamental.
Step16
Play the G string 12th fret harmonic, and match to the high E 3rd fret fundamental.
Step17
Play your high and low E strings, making sure they sound to be the same note. Strum a few chords. Open E and A minor are good, as well as a few others. Go back and recheck or retune if things sound out of order. You are now finished tuning your guitar.