Hmm, It's a hard question, this.
I don't believe Nobodies can be the enemy... see it from their point of view; all they want is to be whole again and become reunited with their hearts. I agree that their methods are far from acceptable, but as Xemnas said, they cannot feel pity, so they are thinking and trying to get their heats back in the most logical and efficient way possible. Plus I love Nobodies
Darkness... now here again, I'm not sure. If we look at the situation in an un-biased view, we can see that light and dark are simply opposite ends of a spectrum, like north and south; you can't have one without the other. So, if darkness was vanquished completely, what would happen to the balance and the World Order? So perhaps darkness isin't the enemy either...
I believe that there was darkness before the Heartless themselves turned up, and without the Heartless, there wouldn't be Nobodies and none of this would ever really have happpened... but they are only acting on instinct so we can't blame them for doing what comes 'naturaly' (not including Xeanort's Heartless here)
So, in my opinion, Ansem the Wise was the unwilling enemy overall... at least for Sora and company anyway.