The best way to tune a guitar, by "ear" or any other way, is to tune it so that all of the A's are in tune with each other--

All of the other notes will fall into place, and every chord, closed position or open, will sound "true"--

The reason that a C chord often sounds off tends to be that, when tuned in the "usual" way, the pitch of the B string is off, which means that the C note, fretted on the B string is out of tune with the C on the A string--

Octaves out of tune are the worst clinkers you can get (the G chord will sound out of tune a bit when the B is off, as well). Fifths, on the other hand, can stand a lot of bending--Thirds are even more rubbery--there are a few different sized thirds in the harmonic overtone series, so there is really no right one--