This is sort of "old business", and very Who-related, so I apologize in advance for those of you who come here for other things and don't care much about pre-Eccleston Who. But before there was the Time Wars that destroyed the Time Lords, there was the War. Same basic premise--the Time Lords were fighting a war against a time-active power just as powerful as they are, but with two key differences--one, the war occurred in the Doctor's personal future, starting the day he died as Gallifrey's enemies finally felt safe enough to move against them. The glimpses the Doctor got of the War (starting with 'Alien Bodies') were scenes from his own personal future, but simply knowing about it warped it and brought it ominously closer.
And two, which is more relevant here, the enemy wasn't the Daleks. In fact, the enemy's identity was never satisfactorily explained. Lawrence Miles, who wrote most of the significant novels in the War arc, intended them to be someone other than the Daleks, but the novel in which he finally intended to reveal their identity was never published. Instead, then-line editor Stephen Cole co-wrote a novel called 'The Ancestor Cell', where they were explained as a collection of technobabble from the dawn of time shortly before the War arc, and Gallifrey, were neatly excised from the line never to be mentioned again.
Lawrence Miles, in turn, went on to write a spin-off series in which the Time Lords and the War are carefully changed just enough that he can use his own concepts freely, called 'Faction Paradox'. In it, the enemy is simply known as The Enemy, with the details of their identity being described as "irrelevant".
As a fan of both Doctor Who and Faction Paradox, I'm not sure this was the right move. At this point, I think that the identity of the Enemy risks drifting gradually into irrelevance if not revealed, while revealing it might drum up useful publicity for a somewhat cult spin-off. I'd really like to see Lawrence Miles (ideally) write a book that explains who the Enemy was intended to be, or if that's not possible due to rights issues (it was hinted at as being an old foe of the Doctor's in some way, shape or form) at least get it out in an interview who it was originally intended to be so we finally can put the question to rest. However, I'll admit that part of my desire just stems from being a fan who hates unsolved mysteries, so I can't say I'm unbiased here. Anyone else remember the Enemy? And do those people want to see it come back and get finally answered? Feel free to make your thoughts known in the comments!