I like epoxy with a bit of wood flour mixed in for body in that type of fill. You can tint it with UC's or dyes if desired but usually the wood flour will darken it enough for my eye. Maybe try a few samples, even drill a hole and try to fill it to see if you like the look. If its deep a through hole i usually tape one side and fill it with a slow setting epoxy, for shallower holes I go with a five or ten minute epoxy.