When the series started people where making a big issue of the whole "I don't want to loose you again" thing that the Dr said about Rose, and some people where saying that the Dr was Rose's Dad and the whole thing got over-analysed, but in the last episode Rose said that the phrase "Bad Wolf" kept following them around and then the Dr said it was probably just a coincidence.
If that is so then, why has the BBC made This website. A website that for all intense and purposes only makes people talk about this more.
I don't think the reference refers to the Daleks because that would be very undalek like. And I don't think it would be Davros because that isn't his style either. I am hoping for the reference means a return of The master.
The reference could even point to the Dr, because the whole of episode 11 was just an excuse to get one of his enemies to call him a killer at the dinner table. Probably so it came across as an analytical observation instead of an insult, but keeping with the fairy tale reference he does have big ears.
EDIT: Link fixed thanks to Bill