I bought the super glue with the application brush from Stewmac for this purpose. I've used it to fill a small ding in a bass guitar fret board which turned out good. I used some dust that that I got from sanding the fretboard put the sanding dust into the ding then brushed the super glue into the dust filling the ding, then a fine sand.
I've also used it for a couple of dings in an acoustic guitar, worked well.
Here's a picture of the bass neck repair, unfortunately I don't have a before picture, the blue highlight shows where the ding was. I was de-fretting a bass neck and fixed the ding at the same time, it was quite a deep rut, now you'd never know it was there
