OrganicZed
Fractal Fanatic
I have been using open string and highest fretted note for several years after reading about it from Rich at ibanezrules.com.
It works really well and doesn't even require a strobe tuner to get very good results.
I was helping intonate a friend's guitar and I came to the conclusion that his low E nut slot must be poorly cut because I could not get it to intonate properly with the open string no matter what.
I'll try the 3rd fret method next time to see how it works.
My only concern with that method as I've experienced with what I'm doing now is that you need to be careful you're not making the note sharp by pressing too hard or accidentally bending it slightly.
Yeah, one of the guitars I intonated has jumbo frets and I took extra care not to bend the notes sharp. Also, I find that it helps to pick lightly because a strong pick attack will pull the note sharp as well.