I sweep up sawdust of the same wood I've cut, mix it with some title bond yellow glue into a paste and fill with it. Low budget but I've had some holes disappear before.

Extra fine (sifted) saw dust mixed with wood glue.
Extra fine (sifted) saw dust mixed with wood glue.
I don't think Bondo is going to work if you want to stain it. I have had the best luck with good old Plastic Wood in the little metal cans. I will say that I bought some Plastic Wood in a tube about a month ago and it suckedDried way too fast so you had no time to really work it in. Stick with the original Plastic Wood brand.
Saw dust plus wood glue is the best choice for hardwood. But the OP is asking about pine. It might work ok for pine, but beware that this mix will sand more slowly than pine, so sanding will dig in around the filled spots.
