"one will still die".
Did he mean Davros or Donna?
Earlier in the episode, Dalek Caan says,
The Children of Time will gather. And one of them will die!
I always believed the Children of Time were the three Time Lords in this episode. Though it's perfectly reasonable to think that it means the Doctor's companions. I highly doubt it refers to a group that includes Davros. Since...
none of the Doctor's companions die, and only one of the Time Lords dies (The Doctor-Donna)
one can assume he meant Donna, no matter which definition you have for the Children of Time.
Here is a better quote from Dalek Caan, even earlier in the episode:
... The Doctor and his precious Children of Time. ...
Seeing that they are his, this clearly rules out Davros, and makes it much more likely that The Children of Time refers to his companions.
He meant Donna; he had been specifically talking about the Doctor's companions when he said that more than once. He's also not the only person to foresee Donna's "death" in some form or another.
He was being figurative, of course; it was only the new, more mature Donna that died by forgetting the past year or so of her life.
From what I gather Caan meant Donna, the "enlightened Donna."
The Donna that the doctor knew and traveled with, the Donna that developed from their time together is dead. While she is not physically gone the consciousness that she had become is pretty much dead. Even if she was reminded of that time she spent with the Doctor her physical body would die from the mental overload, so at that point both her and her Doctor-filled consciousness she was would perish.
I had always assumed he meant meta-crisis ten, given the way he laughed about it at the end. Especially after he mentions that one "will still die".
I suppose that technically "Doctor Donna" dies, but also technically does not. We see that Donna's memories can come back, hinting that Doctor Donna is still there, just hidden. Plus, with meta-crisis ten now being "human", and in the alternate timeline, he can (and will) certainly die for good. "One of them" could easily mean "one of the doctors."
I'm inclined to believe that Dalek Caan was referring to himself - by the actions of the Doctor, he was forced to take actions that resulted in his unprotected flight through the Time Vortex, this being how he penetrated the Time Lock and acquired his powers of prophecy. In my view, this, especially combined with his conclusions from seeing all of the Daleks' history, constitutes a metaphorical "rebirth" which more than qualifies him as a "child of time". Being left behind on the Crucible, his death is all but guaranteed.
Now that I think back on it, my personal opinion on this is that he wasn't talking about the Doctor or Donna at all, but instead he was talking about the Master and the Doctor in the upcoming episodes. I form this opinion in that he said "The Children of Time" I agree this most likely means Time Lords but instead of the Doctor and Donna, who isn't actually a full Time Lord, I think that it was meant to be the Doctor and the Master who were both portrayed as the youngest Time Lords still alive. This would still make sense because in "The End of Time" special,
In "The End of Time" The master is attempting to bring Gallifrey back and ultimately gets him self killed off (presumably for good this time) fulfilling "One will still die."
I used to think that it referred to Donna but have since changed my thoughts to the prophecy referring to Sara Jane, the only companion who actually did die and was also the most loyal, being with Pertwee and then Baker.
She never gave up on the Doctor even after he left her and then in 2006 she was brought back and was as loyal to the Doctor as she had always been and helped save the Earth (as well as securing her own spin-off series.
Regretfully Sladen passed away in 2011. Perhaps the prophecy was a subtle reference to her illness as it was only a few years later that she actually died and consequently her on-screen character Sarah Jane (the most loyal companion) also died.