I find the best way to tune a guitar is using harmonics; Tune the low E string from a tuner or piano/keyboard/whatever. Then touch the low E string lightly above the 5th fret (directly above the fret wire; don't hold the string down). You should hear a chime-like tone that continues if you take your finger off the string. This is called a harmonic. Now, play the 5th fret harmonic on the low E string as described above, and while the harmonic is still sounding, do the same thing above the 7th fret of the A string. Although it takes a while to get used to how it should sound, you should be able to tell if the tuning is way out. If the harmonics are almost in tune with each other you will hear what are called beat frequencies. This sounds like a sort of rhythmic pulsing, the rate of which is the difference frequency between the two strings.
If you've got the low E string tuned correctly you'll need to tune the A string. If the beat frequency is fairly quick you'll need to either tune up or down. Once you get used to it you can somehow tell which string is higher and which is lower (like with DJs' ability to beat match) but at first you might need to experiment by turning the tuner on the A string. As you get closer to the correct pitch the beat frequencies will slow, and eventually stop once the two strings are perfectly in tune. Using harmonics in this way it is easier to hear the beat frequencies than just fretting the 5th fret, and I also find using harmonics gives slightly better intonation than using a tuner for every string if the guitars' intonation is slightly out. Also remember that it's always best to tune UP to a note rather than down, as the tuner is less likely to slip this way. If I need to tune a string down I always go slightly lower than it needs to be and tune back up, using smaller turns each time.
Once you've got the E and A strings in tune, repeat the process using the 5th fret of the A string and the 7th fret of the D string. Again with the 5th fret on the D string and 7th fret on the G string. Next one's a bit tricky to do with harmonics, as the G and B strings are tuned a major 3rd apart instead of a 4th apart like the others. In this case I fret the 4th fret on the G string and tune the open B string to that note. If I have trouble tuning like that, I will also try fretting the 3rd fret on the B string and seeing if the 5th formed with the G string sounds right. It can also be done by playing the 7th fret harmonic on the low E string and tuning the B string to that, although there will be an octave difference that isn't there with the other strings. The high E string can either be tuned using the 5th and 7th frets like the first 4 strings, or by tuning the high E string to the 5th fret harmonic (or open note) on the low E string.
That probably sounds really complicated but I've always found it a really easy and intuitive way to tune; you just need to listen out for the beat frequencies. Working out which string's higher than the other and vice versa just comes with practice. If in doubt, just use a tuner and then check the harmonics to see if you can get the thing more in tune with itself.
Dan
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