I use a Lee Valley's restorer's cat's paw at www.leevalley.com (prod. # 60K21.06). It will get under most of the staples and with it's large surface prying against the wood, with care it shouldn't harm the wood.
And for really stubborn staples, ones that have broken in half, I use the nail puller, Prod. # 64K02.01.
And if that just snaps some off, simply use a fine nail set to set the errant staple wire below the surface (prod. # 23K17.01).
You can then fill all the little holes with a colored latex putty (#80K86.01), but be sure to wipe it off BEFORE it dries with a wet rag.
As always your Most humble servant, Joseph, the Wood Floor Doctor.