If your referring to the scene where he kissed The Doctor, Captain Jack (Can't think of the actor's true name at the moment) explains in the show "Doctor Who Confidential" That he hoped no one would look at it that way.
It was an emotional reaction...to say "goodbye" to someone he more/less now looked on as a sort of "Big Brother". He kissed him in this context... like one would kiss a brother goodbye.
I can't remember which episode of Doctor Who confidential this was, I believe it was one of the last ones aired when the season was comming to an end.
Slashdot Mirror
If your referring to the scene where he kissed The Doctor, Captain Jack (Can't think of the actor's true name at the moment) explains in the show "Doctor Who Confidential" That he hoped no one would look at it that way. It was an emotional reaction...to say "goodbye" to someone he more/less now looked on as a sort of "Big Brother". He kissed him in this context... like one would kiss a brother goodbye. I can't remember which episode of Doctor Who confidential this was, I believe it was one of the last ones aired when the season was comming to an end.