Wow, this has gotten real technical real fast! I hope I don't sound too much like I think I know what I'm talking about, but...

MTed and PoppaGator, you have opened up some important facets of the guitar. Playing in G on standard tuning is NOT the same as playing in E capoed three frets up. One reason for this, I think, has to do with the voicing of the chords (the spacing of the notes).

For example, GBdg sounds differently from Gdgb and from Gbdg', whether played on guitar or piano or sung by a chorus -- even though all are G major triads in root position.

Another reason, I think, is the different shapes made by the chords and scales, and the availability of open strings in the various keys.
In G and C your melody notes sort of fit inside the chords; in D (standard tuning) your hand position and the nature of the scale tends to lead you to play your melody notes on top of the chords. It makes for a different sound.

In part because of my vocal range, I favor D G and A. I particularly like D and A, because I just like the sound of playing up the neck with open strings below. For me that's part of the attraction for the DADGAD tuning. The downside is that my mental encyclopedia of 1001 chords doesn't work!

Cheers and happy pickin'

-HM