On my acoustic I start by tuning the open string to concert, then check the 3rd, 5th and 7th frets and adjust the open string pitch so that all those notes are generally averaged around +0 cents. For instance with the open string at +0, the others might be -2, +4, +6. So I'd pull the open down to -2 to get -2, -4, +2, +4... which sounds smoother on the whole.
Or alternatively if I'm recording in a particular key I'll play the major chords I'm using and test each of the notes and see if anything sticks out tuning wise +-4 or more cents. Then start pulling the open string sharp or flat to iron that out at the expense of notes I don't use much going slightly out.
I don't need to do that as much with my electrics, but it's still an option if I'm not happy with the tuning at any point.
Another thing to note is that for songs where you are bashing the strings hard and fast, tuning a little flat on the bass strings can help. The attack of the note is sharper than the decay. If there is no decay (fast playing) then you have to compensate with a flatter note to start with. This goes double for looser strings (think drop tuning) and Bass.
