My neck through guitar is definitely warmer than my bolt on guitars, it is all mahogany though. It's also got bags of sustain, although I'm not sure to what degree that's down to the fact I'm running it with an active pickup. I tend to feel it's more important in terms of playability more than tone though, I can achieve tones and a degree of sustain which I'm perfectly happy with using either type. To add furthermore to the discussion, my basswood/maple necked RG is definitely thicker and meatier sounding than my mahogany/mahogany ESP, which is more articulate and percussive. This is almost certainly down to the pickups (EMG 707 in the ESP, Invader in the RG). Anotherwords, there's a lot more which contributes to the tone of a guitar than the neck joint.