If you've ever noticed... there is usually something amiss about the treble strings which will cause the 1st position G chord (320003) to sound slightly off when the 1st position D (XX0232) is in perfect tune.  If you monkey with the tuning and get the G chord to sound perfect, the D will sound bad.  This is because the guitar or any other fretted stringed instrument is not perfect.  That is their nature and it has a lot to do with the fret wires running straight across the fretboard.  This dissonance also has to do with our expectations of what "in tune" sounds like.

But never mind the specifics of why this happens.  We just want to get the guitar tuned so that all chords sound equally good (or equally "bad").  This is called "Equal Temperament Tuning".  Plenty has been written about how to get a guitar in tune and there have even been special parts invented to overcome the fingerboard's imperfection.

For beginners-

Because of a tuning machine's mechanics, remember to always tune up from flat - never tune down.  If a string is too sharp, bring the tuning down below where you want to be then tune up to the desired pitch, taking care not to go past the desired pitch.

Also, in the diagrams below I have shown where to play a (natural) harmonic to tune a string to.  To play a natural harmonic, lightly place your fretting finger on the string directly over the indicated fret - don't press the string to the fret.  Now while touching the string at this point, pick the string normally with your other hand and then release the "fretting" finger.  The string should make a chime or bell like sound.

Steps to tune your guitar using the
"Equal Temperament" tuning method: