Adventures in Renovation

So last Thursday I finally pulled up the rest of the linoleum tile. Man, what a bitch that was. But I had to do it that night because there was a community dumpster in my neighborhood that day. I was afraid to dump "building materials" in the dumpster, but when I got there of course there's already tires and plaster and who knows what else in there so I didn't feel that bad about it. Now I just need a few more boxes for the big pieces left.

I've been pulling up nails from the floor for days. Check out this photo. I'm almost done. The question is what am I going to do to the floor when I'm done to hide all the holes. If anyone has any idea of what the best way to do this is, I'm definitely looking for suggestions. Should I fill the holes, sand the floor and hope the stain stains the wood filler too? Or should I fill the holes after I stain and try to match a tinted wood filler with the color of the stained floor? Either way, I'm thinking of staining the floor a dark color to hide it better. But would it be weird to have a different floor color upstairs as downstairs? I think I can pull it off.