The only way I've found to fill holes in floors is with wood. It's tedious work, but nothing else will hold up over time. Besides, I like the look of wood patches in floors. A series of wood patches looks like a history. Wood filler looks like a mistake. Anyway, get some scraps of the floor material, cut shapes to fit the holes, and pop them in. You can taper the cuts so that the patch can't fall through. For larger patches you will need to grab some support from the joists. Another technique I've used is to provide a make-shift subfloor for the patch by securing a larger flat board underneath the floor. This might be difficult if you don't have underside access. Old floors will have spaces between the boards. I once tried to fill them by using an ingenious assortment of string, twine, and small rope, but I didn't like the result. For wide spaces, round the edges with sandpaper. For really wide spaces, make a patch. I'm sure your floor is going to look great. I've never seen an old floor that couldn't be revived. For a final finish I use tung oil. Because it penetrates, it protects the wood without putting a glossy surface coat on it. It's very easy to apply, and you can always refinish or touch it up by simply applying more to any clean surface. No preparation is necessary (after the initial coat).