**** Spoilers****
I thought the Doctor was trans*dimensional or something. Sure does have a "thing" for the TARDIS too. Two hearts? 1 male, 1 female perhaps?
I also feel like they have hinted the Doctor is Transgender, more so in the 2005 and later episodes. Look at Missy/Master. I mean its regeneration, but its like a transgender dream. I love it.
Matt Smith, upon regeneration / introduction of his character, grabbed his hair and squealed something like, "Hair!, I'm a girl...?? "

Missy says something about being there when the Doctor was a crying little girl.

Something was going on with the Doctor and Captain Jack...(face of Bo?). or was that just Jack crushing on the Doctor?
Clara fooling the Cybermen that she IS the Doctor and has been all along, and almost fooling me for a second too. "I was like.. WAIT WHAT?

"
OH!!!!
and K9 always calls The Doctor, Master... I always wondered...
-Jade