"Bad Wolf" has appeared in every episode of the BBC's latest series of Doctor Who, with additional cryptic mentions on official web sites. An episode later this season, entitled "Bad Wolf," is likely to provide an explanation.

I'm not familiar with the extensive backstory in the Doctor Who universe that precedes the new series, but I'd be surprised if Bad Wolf was anything but The Master, and the episode "Bad Wolf" involved anything but The Master disguising himself as the Doctor and doing bad things. Hints all imply the Doctor is being mistaken for someone known as "Bad Wolf", and Rose's introduction included an obvious Red Riding Hood reference.

The official in-joke web sites are pretty fun. See WhoIsDoctorWho.co.uk, run by present-day Earth character Mickey.