Whoa whoa whoa nereo what if he's got some beautiful old growth floorboards on the ground there?
I agree that replacing the floor and examining subfloor might be the best option. But if this is old water damage from a problem that is determined to have been remedied, then splicing in new flooring could be the best way to go.
This Old House has some good videos on this topic.
Yes, you can nail by hand with the help of a nail punch to help you sink them all the way in so that the next floorboard can snug up in there.
What you'll end up doing is probably face nailing the last board after you rip the tongue off it.
Then you can use a buffing type sander (a full on hummel sanding is what the pros would do for a perfectly flat floor, but for a DIY project you can feather it in just fine with a buffing type sander depending on your ability to seamlessly match the existing finish).
If it's an old house, look for salvaged materials at a lumber yard or a salvage store. Old homes had skinnier floorboards than the 2 1/2 board commonly sold today, and the wood has aged and become darker so newly milled boards probably won't match well.
If all that sounds like too much, maybe Nereo's right. Except about the cost, unless he's talking fake wood laminate. Solid hardwood + sanding & finishing will be more. Prefinished is kind of ugly with it's bevels but at least it's better than fake wood.