I use the Starbond colored CA for that as well.  They have both black and brown tones and different viscosities too.  For fine cracks the thin is better.  I generally prefer the brown because it looks more natural than the black with most woods.   If the hole does go all the way through, a piece of tape on the bottom is advised.  For deep cavities, I usually pack some saw dust in the bottom for filler but not all the way up to the top because I don't like the particle board effect that sawdust sometimes creates.  You can use clear CA for the sawdust and then just top it off with the colored CA.  Let the CA with the sawdust cure before you top it off with the colored CA.  You can use an accelerator to speed up the cure.  

--Nathan, TX. Hire the lazy man. He may not do as much work but that's because he will find a better way.