Without knowing the specific end use and history of the wood or the scale of the project I can only give you three general techniques and you can choose which one suits your needs best.
- Paste Filler.
This comes in a variety of forms but essentially its exactly what it sounds like. It hardens to a sand-able surface, takes stain and finish more like wood than other fillers and some varieties can be applied in large quantities (hardwood floors filler). Some are water based, and some use solvents (acetone and MEK). In this case (and this case only) the water based is just as good as solvent but not if it's for exterior use.
- Oil Putty.
This is the finish carpenter's choice for puttying nail holes in finish grade trim and other small repairs and fills. It comes in a variety of colors that can be mixed to achieve any shade. The putty is applied after finish so it goes on soft and stays flexible. Its great for small fixes but would be impractical to patch large voids or large areas.
This is just a clear, two-part adhesive tinted with pigment to create a hard, durable, stable patch, here's a helpful link: West System. This method is great for filling things like knots and surface checking. We primarily use it on reclaimed lumber to fill the defects prior to finishing. Epoxy can be used inside and out, on small or large areas but it is the most expensive of the three options.
Whatever your situation, one of these three should work. The only general advice I can give you is, whatever method you use, make sure your fill is at least as dark or darker than the wood. Light filler really stands out. The catch is that many woods (cherry, fir, mahogany) darken significantly over time so you have to adjust by eye and your gut. Cheers!