Earlier in this TV segment we installed a threshold between an old and a new floor. In that case we actually cut away to a flat base that allowed us to put our threshold down flat. If you cannot do this or for some reason need to fill in a low spot in a floor before putting in the threshold itself, there are several different products that will do the job, depending on how deep the hole is.
If the hole is fairly deep you will need to use a large quantity of filler. Here you are best working with a self-levelling concrete. This stuff flows out in a very plastic manner, if you don't let it sit too long in the bucket, and will feather out to a fine edge. It is good for all kinds of filling, but because of the trouble of mixing it, I only use it for deep or large jobs. It will not hold up outdoors and should be covered with something to protect it, but it makes a good indoor sub-floor.
LePage makes an excellent non-shrinking product called "Exterior Wood Filler" that can fill up to an inch or more thick. Because of it's cost, I will use it where I need about 3/8 in depth but I don't have a big enough expanse to justify the self levelling concrete. This is the only one of the fillers that could actually be tinted to match wood on the floor and be used as the final surface with a varnish over the top -- but not in heavy traffic areas.
When you have about 1/8th of an inch to fill, I will just use PL Premium adhesive. This is a construction adhesive that dries rock hard, so it will act like both an adhesive and a filler at the same time, but because of it's cost I wouldn't use it to fill a large hole. It is however, the strongest of all three products, once cured. Be careful because it will stain any wood it might be spread on -- so don't let the caulking gun drip where you don't want a dark brown stain.