whats the difference? i know bolt on is the neck is held by bolts, but what about neck-through? any difference between the two?
Neck through is where the neck of the guitar goes the full length from the headstock to the strap button, and then two pieces of wood called wings are glued on to the sides of the neck. Bolt-on is just what you said, it's a guitar body with a removable neck held in by bolts.

Bolt on:

Neck Through:
Some say that bolt-on's have a bit more snap and emphasize overtones.
Some say that neck-thrus have a bit more sustain and emphasize the fundamental tone.

This is highly subjective and is only a theory. I believe it, but it don't mean you should.
<Insert Witty Comment Here>

1981 Fender Lead I Seymour Duncan humbucker, Mesa BoogieIIIRectifer, MKIIRhodes,PRS
There's bad neck throughs as much as there's bad bolt ons. A good bolt on is as good as a good neck through.
The preference lies in feel, and for a lot of people, pure snobbery.
Fender Precision Bass
Fender Jazz Bass
1967 Fender Coronado Bass II
Warwick Star Bass
Squier Precision Bass TB
Quote by Deliriumbassist
Only real difference is look and cost.

And feel if you want to go into blocky heels vs smoother neck throughs, but yes pretty much just looks and price.

The sustain arguement is unprovable since there's no 100% perfect neck joint, and testing the differences would be nearly impossible. And any difference in tone is negligable at best.
Composite Aficionado

Spector and Markbass
mostly feel. I have a bolt on and a neckthrough, unfortunately ones a 4 and ones a 6 so its really hard to give a fair comparison.
no sir away a papaya war is on