Our favorite flooring book talked about using putty to fill in the nail holes in the floor. This doesn't seem like a terribly common practice--at least based on our attempts to find floor putty. We were disappointed by how few options were carried by the Home Depot where we were renting the floor sanders, but we couldn't find any other area stores that carried any putty. Conversely, when we looked for putty products on the internet, we were overwhelmed by the number of choices.
P confronts this type of problem all the time at work--which of the myriad products available will be fulfill his company's needs? What are the specs on the product? What kind of wear and tear will it stand up to? So he approached this just as he would with his employer: he phoned a major distributor that carried a large number of these products, and asked which would best suit our needs.
They recommended only one for our purposes: Woodwise Wood Patch. So we ordered ourselves a gallon, and P got to patching.
We initially tried patching before sanding, since the patching compound itself would need to be sanded smooth. But P quickly discovered that this wasn't the best approach. Our floors were stained a darker color, and we were planning to sand off the stain and leave them in a natural color. But the process of working the putty into the holes caused bits of the old stain to chip off and get mixed into the putty, leaving it a darker color than we wanted. So the puttying had to be done after the initial sanding to remove the finish, but before the final sanding to smooth the floors--that is, between our second and third weekends of sanding.