For my Martin D-18, it’s D major. Anyone else noticed a particular key that seems to resonate better than any others?
Oh - heck yeah. My Taylor 812C (concert-sized guitar - like what Clapton played for “Unplugged” with a cutaway) plays best in A - the question is: how much of that is due to:
a) my ear - might I hear things in A better - detect harmonies
b) playing it a lot - I play a lot in A - doesn’t every self-taught budding rock n’ roller learn the minor pentatonic blues scale in A first? Maybe I “broke in” the guitar in A so it sounds better in that key
c) the materials and construction of the guitar
I dunno, but I definitely hear it.
I just read a great article (but I’ll be darned if I can remember where) about a guy who recently bought TWO vintage Martins. Ironically, they had sequintial serial numbers. One was played almost never and the other was used in a band and was played a lot. With new strings, they were indestinguishable in a blind listening experiment. The (semi-scientific) conclusion being that wood doesn’t have a memory for any specific key.
But I swear mine sounds better to me in “A”. 
Hear it! Hell, I bet you feel it! I know I do.
It’s not that wood would have any “memory” for a certain key, but any given object constructed out of any material whatsoever will resonate in a certain way, with its own tonal fingerprint.
Especially in non-manufactured instruments like high-end classical string instruments. So naturally some notes in particular will just resonate well on individual instruments. The reverse is called a “wolf” tone, where the instrument resonates very poorly on a certain tone. I have one on my viola, F natural above middle C. Sounds dull.
Instruments with mostly well-resonating tones are highly prized.
I wonder if it isn’t due more to the fact the D is easily played in the open position than how it resonates. But if you want to test that, tune down a half a step. If it’s the resonating qualities of the wood, you would have to play everything up a half step (D#) to get that quality that you love. But I suspect it will sound as good as you know it when you play that open D chord (now sounding a D flat).
Open strings resonate better than fretted ones. So open position chords sound nicer and fuller.
it also has to do with the wear on your guitar’s neck. with my guitar, or with any guitar for that matter, i can tweak it slightly depending on what key i’m playing in (i.e.–taking the B string up a fraction of a note to play in G major, from E major). this is due to slight changes in how straight the neck is. a good way to tell if your neck needs to be adjusted is to play an open string, and then play it on the 12th fret (octave). if the two notes sound good together, you’ve got a nice guitar. if they sound off, you may want to take that baby in.
yeah - two factors that can affect whether a guitar sounds good in general, or better on specific chords, is whether the neck is out of true (bowed forward or backward, or to one side) or if the string compensation is off. Electrics have Tun-o-matic bridges (Gibson or Gibson-like guitars) or some variation thereof, with little saddles to adjust string lengths to get the right amount of compensation; most acoustic just use a slanted bridge with a special notch for the B string.
All that being said, I think the OP has more to do with the tonal/resonance properties of a wooden instrument than whether the guitar is set up correctly, although that can have an impact, too. I think jpeg jones stated it best with his/her description of a “tonal fingerprint”
D15 owner here.
first thought the guitar was better sounding that the D28 and D25? of my brothers. but after a year I like his sound better. the question is did my ear change or has the guitar changed. of course new strings.
2nd question: medium strings. how much tonal difference are you going to get with different brands and compositions. I am using martin phosphorous bronze . always have.