Deep scratches: If the scratches go below any stain then first touch up the stain. Either you know exactly what stain was used or you will need to experiment on some oak scraps. Then, the only thing I can think to do is to try to build up the finish (urathane), up to the height of the rest of the floor. I know that a trick that some body shops use for deep scratch patching is to just keep adding layers of paint to the (lower) scratch until it is nice and flush with the main paint surface. Then they just buff it out some and they are done. It is important that you know whether your floor is high gloss or satin, oil or water based finish, in order to get the best match. The trade secret of some body shops for being able to paint ONLY in the crack is to use the ripped end of a paper match as a mini disposable brush. 3, 4, 5, 6 coats later it will be flush and you will not notice it.
Smaller surface scratches: For small surface scratches that are not deep at all, I usually use "old gold" brand furniture polish/oil and just rub a little on. Small scratches seem to be unnoticable after doing this. Caution: Rub excess polish off the floor and be careful as it can be quite slippery for a couple days.