Much depends on how wide and deep the cracks are and what your project is. There are any number of wood fillers that will take stain and paint. If the crack is wide, though, any of the fillers that I have tried will be visible after staining. Paint will cover them, though. For painted work, Milliput is excellent. It is a two-part moldable epoxy putty. It does not stain well, though. If you are limited to big box stores, both Bondo and Dap make fillers that will take stain and paint.
If you have specialty stores near you, ask for their advice.
If you have specialty stores near you, ask for their advice.