As Davies has told the New Jersey Star Ledger, he originally designed the "Jack is Boe" tease as a fun, running joke that would come up on occasion, simply because both characters are extremely long-lived. "It wasn't exactly planned," Davies says about Captain Jack's wham line in the season 3 finale. "I did spend a long time thinking about Jack's immortality, and one day it occurred to me there was another immortal character on the show. It made me laugh ... I have my own personal theories, but the moment it became very true or very false, the joke dies."
Alas, other people involved with the show didn't share Davies' love for comical ambiguity, and so, the joke died. "Last of the Time Lords" came out in 2007, and in its episode commentary, executive producer Julie Gardner flat out told the showrunner to "stop back-pedaling" about the Boe-Jack connection. In 2008, she happily confirmed that the two characters are one and the same at San Diego Comic-Con. David Tennant (who played the Doctor in the episode) and Barrowman have also gone on record embracing the theory. Oh, and the show's production team sneakily made Boe call the Doctor an "old friend" in post-production for another season 3 episode, "Gridlock," as if to further imply that the two know each other from way back.
So, regardless of Davies' original intentions, it sure looks like people are determined to present the "Jack Harkness is the Face of Boe" thing as canon.
