You can get pretty creative with crack or gap filling. About anything in the spice aisle at the grocery store can be used (pepper, mustard seed, etc). Coffee of course too. Crushed stone, Inlace, turquoise and other rock and coral products can be used. Another one I'm going to try is charcoal.
I've heard of people mixing them with epoxy but I always use CA glue. I start with thin CA glue to run all the cracks and voids and generally stabilize the tiny parts of the cracks or holes. Then I use medium thickness CA glue to get into the remaning small nooks and crannies. I use thick CA or gel CA to fill the bulk of the hole and I push the coffee into the gap with my fingers. After putting the coffee in some voids are created where the glue doesn't flow around it, so thin CA and medium CA are used to fill those small spaces. After all that has set I turn the piece, frequently stopping to add thick or gel CA into the remaining pinholes that inevitably appear. It takes forever and takes a bit of patience. Don't use slow-setting CA, use the hot stuff that dries in a minute or less and cures in five minutes.
The CA is hard and clear, pretty much like acrylic. So it sands, turns and polishes well.
Spray activator is great for this little process. You have to be careful with it because it will sometimes "frost" the CA.
Thanks for all the compliments! Doing this allows you to use wood you might otherwise throw away and make it unique looking at the same time.