First, kudos to you for wanting to use your ear to tune - if you don't practice this essential skill as much as possible, and instead always start with a tuning device, when the chips are down you'll be fff* - well, in a bad way. It's great to check yourself after tuning by ear with one, though.
So - it depends very much on the music. If you are playing with other instruments with fixed pitches (for example, keyboards), they will almost always be using "tempered tuning". This ensures that, no matter what key (C, A-flat, F#, whatever) they are in, they are all equally in tune (or out-of-tune, actually - for TMI, Google "Pythagorean comma"). So you had better tune your guitar using tempered tuning as well - use the classic fifth-fret pattern (or a usually more accurate and reliable approach using octave harmonics).
If you are playing jazz or classical solo guitar (as I do), particularly jazzy or contemporary pieces (that use lots of different keys), then you'd better temper your tuning as well.
BUT - if you are playing by yourself, or singing with the instrument, or playing songs that stay in one key, then you can use a much purer tuning approach - the fifths won't be flat, the thirds can sound less muddy - that, I'm guessing, is what the fellow was doing that tuned to a particular chord. For example, when I play flamenco, I usually tune to open fifths and octaves on E and A, since flamenco, for all its complexity, stays always very close to "open string" harmonies on the guitar, and relishes the dissonance that comes with a purer tuning. Using the harmonics at V and VII will give you this purer result as well, but can get tricky.
So, to build your ear and emulate your friend, play around with getting a chord sounding right, and checking your results. Then get two different chords to sound right, and check your results. Using E and A will give a purer sound, E and C a more tempered result.
Hope that helps - and keep tuning using your ear!