Hi, Byron. I am familiar with people using hardening fillers like Minwax's 2 part product or several brands of wood putty. Most of the wood fillers do not take stain well and you do not want to use hardening fillers in the spaces between boards as this will lead to further cracking with expansion and contraction.
There are also the wax-like fillers that never harden. Minwax also sells these and they are available in small jars in various colors. The colors can be mixed and blended in small areas like where you have set a nail. Most people try to mix a color as close as possible to that of the finished wood. I'm not familiar with any other types.