Others have piloted the TARDIS in the past, although rarely with any degree of skill. Romana (another Time Lord) did, and I'm fairly sure Nyssa did too at some point.
Tegan also apparently did, but that was really the Master controlling it indirectly (Castrovalva).
Geek mode OFF
Dear Drew, Torchwood is not Season Two's "Bad Wolf". There was another, more discreet repeated word this year, but its meaning was not resolved. Worked it out? It's in "School Reunion", "Rise of the Cybermen", "Idiot's Lantern", "Impossible Planet" and "Love and Monsters (boo)". That's all I'm giving you, though I have a feeling it's connected loosely with "I was a Dad once".
I've been racking my brains on this, and I'm getting nowhere. The only thing I've come across is the mention of the term "lonely" and "alone" with regard to the Doctor. "Lonely God" and "Lonely Angel" were both mentioned. But that doesn't match your list of episodes. I'll keep trying.