One of my great frustrations with guitar is that guitars never quite sound in tune. Something always sounds off. I understood this to be due to the inharmonicity of (plucked) stringed instruments, and also due to the inherent flaws of a fretted instrument.
One of my first attempted solutions was to tune the guitar to an important chord in the song I was playing, using electronic tuners. I would tune to the chord I most wanted to be in tune (or in other words, the chord that annoyed me the most if not in tune), which was usually the chord before the chorus. However, this is not a very satisfying solution, and you still constantly feel like things are not in tune.
Now, when you hear a guitar, what you perceive as the "pitch" is generally not the fundamental but the 1st overtone (the octave above the real fundamental pitch). When you are tuning and your ear is focused, you perceive both the fundamental and the 1st overtone and probably the 2nd and 3rd overtones contribute too. For the low bass strings, the inharmonicity can be significant, and this is why it seems impossible to tune and strings seem simultaneously too low and too high, no matter which direction you adjust.
THE SOLUTION, my dearest friends, is to tune, by ear, to the 12th fret, or octave, 1st harmonic!!! You are tuning to the 1st overtone of the harmonic (as it is perceived more strongly than the fundamental pitch), which is the 3rd overtone or 2nd octave of the fundamental of the string. By doing this, you are essentially tuning your guitar so that the overtones are in tune, which is similar to how they tune pianos; and thus, in normal playing (when you are not really perceiving those fundamental tones), everything sounds in tune! To my surprise, moving up the fret board in different positions still sounds in tune too.
Et voila. :^)