One trick to using an electronic tuner is to tune the to the notes you use most often, not necessarily the open strings. It's more important to me to have the G notes at the third fret on the two E strings in perfect tune than to have the open E notes there. If the E notes are off a smidge I can live with it. But if the three G notes in a regular G chord aren't in tune with each other it'll drive me bonkers. I also tune to the D note at the third fret of the second string, not the open B note.

Of course, if your intonation is really out this little adjustment won't work. The best you can do then is compromise and have, say, the fretted note just a bit sharp while the open string is a bit flat. Or you could just consign such a guitar to the land of guitars-suitable-only-for-slide-playing.