In order to fill the spaces between your floor boards, you'll need some wood filler. We stumbled on Elmer's Wood Filler, which comes in two convenient sizes depending on the size of your job. This stuff works great. Like their school glue, Elmer's wood filler is water soluble, which makes for super-easy clean up (no worrying about getting the filler all over your floor -- you can just clean up at the end with a mop, water and a little elbow grease). To apply the filler, simply use a spackle knife and smooth some of the filler over the cracks, sweeping perpendicular to the crack/hole. Keeping smoothing the area over with your spackle knife until the filler is flat with the surrounding area, applying more filler as necessary. Since the filler will reduce a little bit as it dries, you may need to come back with a second application for deeper crevices. Once we finished applying the filler (and cleaning up), our floors looked like this:
We let the filler dry overnight before we went back over it with a Mimwax wood finish stain marker (we used "Early American" finish), which works just like any other paint pen. Staining the filler was actually far more tedious than applying it in the first place (though clean-up was -- as usual -- my least favorite part of the whole process) and I managed to get it all over me. Because of the huge area we had to fix, the entire process took us several weeknights and a good bit of a Saturday, but smaller jobs could easily be tackled in an afternoon. But the finished product turned out pretty well I think:
In the above photo, you can see how beat up our floors really are in some places, but I think the filled crack blends in pretty well, don't you? As a warning about the Mimwax stain markers: they don't go very far; in fact, we ended up running through a half dozen of them during the course of the job, so I'd suggest buying several if you're doing anything more than a minor touch up or two. Additionally, I thought the stain was rather transparent, so we ended up having do go over most areas several times to get the right depth of color.
Now that we've finished the project and our cleaning service thoroughly cleaned the floors, I'm really happy with the result. It took a good bit of work, but by doing it ourselves, we saved a lot of money on labor and in the end spent less than $100 on the necessary supplies. My only regret is that I didn't do it sooner!