I just watched "The Name of the Doctor" this afternoon. As I recall, GI mentions that the Doctor has done horrendous things, but in an incarnation (incarnations?) known as "The Storm", "The Beast" and "The Valeyard".
in "The Parting of the Ways", the Ninth Doctor tells the Dalek Emperor (IIRC): "You know what they call me in the ancient legends of the Dalek homeworld? The Oncoming Storm."
I know that "The Oncoming Storm" and "The Storm" are not quite the same term, but is it possible that Nine's knowledge of the "Storm" name and GI's familiarity of that name suggest an incarnation of the Doctor (although by another name) that existed before Eleven's incarnation?
Either way, based on what I have seen, I agree with those who are leaning towards Hurt's Doctor as being the Time War Doctor, and existing between McGann's and Eccleston's incarnations. Also, is it possible that in "The Trial of a Time Lord" The Master's is lying when he says that The Valeyard is an amalgamation of darker natures of the Doctor's twelfth and final incarnations? Ret-conning yes, but it could work. Maybe a desperate Time War Doctor needed to steal the regenerations in some earlier, unsuccessful attempt to end the Time War....
In any case, I thought this episode was excellent! Packed full of Goodness! Can't wait to see what is next!