I know the structural differences in a neck-thru as opposed to set neck, but i dont really know the tonal charactaristics. If I am looking for a guitar with loads of sustain and crystal clean tone, which neck type should I go with? I like the idea of neck-thru necks more, but they just dont make that many guitars like that.

neck thru is where the neck is one long piece of wood with two wings attached to either side of it. this has minimal heel. set neck is where the neck is glued onto the body. this has a heel which is very small unless its a PRS. if you want long sustain you might get a neck thru and have a t.o.m and string thru. and your tone is dependant on your amp
You can get a good set neck that sustains just as long as a neck-thru. The body and hardware affects sustain too. Basically, the more of the strings vibrations transferred into the body = more sustain. Fat bodies tend to provide more sustain (ie Les Paul, anyone?). An Angled headstock also helps, cos it creates a good tension at the nut, so the vibrations can travel into the neck and body.

If you want a neck-thru, check out Jackson Soloists. I think most of them are neck-thrus.