ze kink
THE BLACK WIZARDS
I haven't noticed a difference in sustain personally, but I do obviously notice a difference in tone. The bolt-on guitars I've owned have had a sharper, "snappier" tone, and more attack overall. Acoustically, they don't usually sound as loud and don't resonate as much, but plugged in, there's no difference. Set-neck and neck thru guitars I've had have been pretty much the same, but on neck thru guitars, the neck wood seems to affect the tone a lot more, which is probably because everything (=pickups, bridge) is essentially mounted on the neck. Neck-thru and set-neck guitars usually have a better upper fret access, but it's not like bolt-on's are hard to play up there, especially if it's shaped well (like on my friends Ibanez J-custom RG7). Both neck-thru and set-neck are sort of "crunchier" and have a "fuller" sound, but less attack. They are usually louder acoustically too, and seem to resonate better.
This is just IMO and subjective, and based on what I can remember of the guitars I've had.
This is just IMO and subjective, and based on what I can remember of the guitars I've had.