Given the intonation issues on any guitar, my approach is to mainly tune the D string to a reference note (say, on my electronic tuner, a recorded song, or the person I'm playing with) then tune the rest of the guitar "to itself".
Also consider the song: is it mainly played down in the open position, or further up the neck? Any guitar tuning is a compromise so aim for the fine-tuning that sounds best for what the particular song demands.
Herewith my procedure, assuming you're retuning the guitar from standard tuning to open D:
1) Initial tuning
- The A and D strings are already there. Just check they're 5 frets apart, then refine by matching the 5th fret harmonic on A string to the 7th fret harmonic on D string.
- Drop the lowest string a whole step from E down to D. Fretted at 7th fret it should match the A string. Now double-check the lowest string by playing its 12th fret harmonic against the 3rd string (D string) played open. Fine tune till any beats are gone.
- Now drop the G string (4th string) down a half step to F#, checking it against the 3rd string / 4th fret.
- Now drop the B string (5th string) down a whole step till it matches the 12th fret harmonic on the A string (2nd string)
- Now drop the high E string (6th string) down a whole step, matching it to the 5th string at the 5th fret and double-checking by matching the 6th string 7th fret harmonic to the 5th string 5th fret harmonic. Finally, check the open 6th string matches the 12th fret harmonic of the D string (3rd string).
- At this point, you've reduced the tension on several strings and are likely out of tune again due to neck relaxing and/or the tremolo readjusting. Repeat the steps above, in order, at least twice, until the strings all sound right in that sequence.
3. Finer points
a) The most obvious guitar tuning/intonation issues tend to creep in on the 3rd of a major chord. Procedure:
- Strum the guitar all open (no fretted notes). Listen for any off notes, particularly the F# (4th) string.
- Compare the F# to the low D (1st) string fretted at the 4th fret; adjust the fretted low D to match the F#.
- Compare 5th fret harmonic on the low D (1st string) to the high D (6th) string played open; adjust the high D to match.
- Repeat with another open strum
- Now check the sound by strumming the 12th fret harmonics across all strings, and by playing straight barres at the 5th, 7th, 9th and higher frets. Tweak any off-notes accordingly.
- Finally, if you really want to optimize for any position other than open strings, apply a capo at the desired position and tweak again. Just be sure to do this last, after you've tuned without it, as the capo will both introduce string friction and disrupt the way the instrument responds to the neck-tension changes involved in moving from standard tuning to open D.