The word Bad Wolf appeared several time throughout the first series in Doctor Who.
The words 'Bad Wolf' appeared in the following episodes.
Rose - The Autons mentioned it to The Doctor.
The End of the World - Moxx of Balhoon spoke the phrase "This is the Bad Wolf scenario"
The Unquiet Dead - When Gwyneth read rose's mind she mentioned the "Big Bad Wolf"
Aliens of London - A kid gratifies 'Bad Wolf' on the TARDIS
World War Three - The same kid cleans the graffiti off the TARDIS.
Dalek - The name of the landing Helicopter at the start is 'Bad Wolf One'
The Long Game - A TV channel is named Bad Wolf TV
Father's Day - There is Graffiti on a wall near wheir The Doctor and Rose are watching Rose's father Pete being ran over.
The Empty Child - Nancy tells The Doctor about his big ears and big nose (little read riding hood)
Boom Town - The Doctor notices that the power plant built in Cardiff has the code name ''Blaidd Drwg'' and mentioneds that he has heard that word before.
In the final two episodes of the series Bad Wolf is mentioned several times and the reason behind the words are explained.