Time after time the words Bad Wolf appeared on our screens - leaving viewers open with clues.
It was all revealed in the final episode of this series, scroll down and see the developments.
ROSE
The Nestene is supposed to mouth the words when it sees the Doctor

THE END OF THE WORLD
The Moxx of Balhoon is talking to The Face of Boe, he is heard saying: "this is the Bad Wolf scenario"...

THE UNQUIET DEAD
Gwyneth is talking to Rose, and talks about the things Rose has seen including "the big Bad Wolf"...

ALIENS OF LONDON
The words "Bad Wolf" have been spray-painted on the side of the TARDIS... There is also a subtle reference to the three little Pigs story, in the form of the Doctor chasing after the Pig in the space-suit.
WORLD WAR THREE
The American news-reporter in this episode, was named as Mal Loup on the whoisdoctorwho.co.uk website. - Mal Loup is French for Bad Wolf...
DALEK
At the very start of this episode, Van Statten's helicopter descends with a loudspeaker saying: "Bad Wolf One descending"...

THE LONG GAME
When the TARDIS crew is being introduced Satellite 5 with Cathia there is a TV screen with The Face of Boe on it. At the top-left is a station logo that says "Bad Wolf TV"...
FATHERS DAY
On the wall littered with flyers, is a smiley face with the words "Bad Wolf" written on it...
THE EMPTY CHILD
This is probably the most subtle reference in the series so far, we see Nancy talking to The Doctor about his "big ears" and his "big nose", both references to the Little Red Riding Hood story.
THE DOCTOR DANCES
Captain Jack captures a German Bomb called "Schlecter Wolf", which means "Bad Wolf"...
BOOM TOWN
"Margaret" Slitheens project is called the "Blaidd Drwg" project, which translates from Welsh to English as Bad Wolf. The Doctor then says to Rose "Everywhere we go, two words, following us - Bad Wolf", before quickly brushing it off as nothing.
BAD WOLF
Bad Wolf Corporation on Satalite Five appears on the screen

THE PARTING OF THE WAYS
When Rose gets back to Earth, the words are sprayed on to a pavement and all across the area where she stands. It is reveated that Rose and the TARDIS are Bad Wolf after she goes back save the Doctor and absorbs a lot of energy from the heart of the machine to make it go back