Honestly, I'm weird about it. I'll use a tuner, but never fully trust it.
I'll get my high E in tune.
Tune the B by fretting at the 5th fret (unison with the E), and also by the E and B open.
Tune the G by fretting the B and E in the 3rd fret and making sure there's nothing ugly there.
Tune the D with the Octave at the B string, 3rd fret.
Tune A with the octave at the G string, 2nd fret.
Tune E string with the octave at the D string, 2nd fret.
My friends used to hat that I do it this way, but I feel like it just gives me a better range of intonation that just using the 5th fret thing, since I'm tuning with parts of chords.
I'll use harmonics, too, especially on the bass.