#1
Ok, I always had trouble tuning by ear. I've used a tuner always, but I've been trying recently to tune by ear. I can learn some songs by ear, but tuning bugs me. The guitar sounds in tune, but I guess I'm a perfectionist so I always tweak the tuning knobs a little more if one string sounds to be vibrating more or less than the other one.

Usually I will downtune a little and then tune up until pitches match. My friend tunes using harmonics, anyone know how to do that?
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#3
On the E,A,D and G strings.... Low E 5th fret harmonic matches A 7th fret harmonic, same for the others i mentioned.
To tune the B string and the high E string, hit the 4th fret harmonic on the G string, which in turn should be the same as 5th fret harmonic on the B, which in turn is the same as 7th fret harmonic on high E.

All this helps, only if you have one string tuned to concert pitch... so tune the low E string with the tuner, and work from there

Hope it helps ya
#4
Listen to a million perfect fourth intervals and then you're golden! Well you're golden once you reproduce that subtle vibratory balance while tuning.

My father taught me how to do that when I was wee by doing it a few times, he'd say "Listen, sounds like the two sounds are warbling in and out unpleasantly." And then he'd tune it correctly, very slowly "See now how it's coming together!" And boom.
Hard to explain, but listen to that warble!
#5
I find tuning by harmonics loads easier - it still helps to detune a bit first though.