I've used bondo under paint (it costs a fraction what Minwax epoxy filler does and it works just as well), but I know from experience that it doesn't stain well.
On the 'wooden cobblestone' episode, they recommended sawdust too, 2-1 with sealer. I've tried it with shellac, using router chips in with the dust, and it works OK but tends to be softer than the wood around it. It's not quite what I want.
Someone offline recommended Durham's water putty, which I'd used in the past but forgotten. Apparently, you can mix it with paint or stain (latex) and I may give that a try.