Typically the thin CA soaks in deep and sets up fast. The thick version cures slower, soaks in less and fills in gaps. The medium version is usually the best of both worlds.

I usually use the thin for all of my balsa to balsa frame up work. My unscientific testingrevealed that the thin stuff makes for a strong joint if the fit is good. The wood will normally break before the joint fails. This method also builds somewhat lighter, especially if you do not use CA to fill in poorly fit joints.