Torchwood was the running theme through series 2, like Bad Wolf was in S1. There were probably more references to it in S2 than just Fear Her/Impossible Planet/Satan Pit (they said they were collecting data for the Torchwood Archive - and that was centuries in the future) and the final two episodes where it was revealled what it was. (Although now I've written it down that is 5 out of 13 episodes, so there might not have been many more.)

I wonder if somebody has made a list of when/how it was referenced?