I just watched The Doctor Dances (Doctor Who, S01E10). Captain Jack Harkness said the Time Agency took two years worth of memories from him.
ROSE: So, you used to be a Time Agent now you're trying to con them?
JACK: If it makes me sound any better, it's not for the money.
ROSE: For what?
JACK: Woke up one day when I was still working for them, found they'd stolen two years of my memories. I'd like them back.
ROSE: They stole your memories?
JACK: Two years of my life. No idea what I did. Your friend over there doesn't trust me, and for all I know he's right not to. Okay, we're good to go. Crash site?
The issue was never brought up again in either Doctor Who or Torchwood.
So what was erased from his memory?