Tightbond also makes a translucent glue which is very hard to see. Best used without stain or dye though as it absorbs the color faster than the surrounding wood leaving a dark line.
How can you hide that dark line before applying finish? I've got one I'm struggling with right now. It's in a very visible place .............just behind the top tang on a 1889 Remington, where a piece of walnut has been inletted, to fix where a large chunk had chipped out behind the tang. It's a solid repair, but just needs to be hidden.

SRH