The BBC recently did a study on the portrayals of LGBT characters in TV, and came to the conclusion that such roles need to be diversified beyond simple "gay" storylines. Much praise went to Doctor Who, which has always been extremely astounding when it comes to treating LGBT characters as, well, characters and not stereotypes. That being said, look for my upcoming article "10 Most Tacky Gay Jokes in Doctor Who."
All kidding aside, you really have to give the show credit for the way it will allow a character of non-hetero persuasion to act normally with that aspect of themselves being simply another trait. The bi or omnisexual Captain Jack Harkness is the best known example, being a lighthearted horn dog, a troubled immortal, and a pragmatic soldier all at the same time. There are plenty of more minor and casual players, like Vastra and Jenny, Lady Cassandra, and the Cassini Sisters, and the fact that they drop in and out of episodes so seamlessly is testament to Doctor Who's status as a bastion for realistic LGBT interactions on television.
It did make me wonder though... how does one classify the sexuality of the Doctor himself?
To make this easier, we'll focus on the three modern Doctors. The first seven displayed almost no interest in romantic relationships with their human companions. Eight did, but there's not really enough examples to pinpoint an examination.
The Ninth Doctor remains among the most troubled of all the Doctors, and is probably a textbook case of PTSD after surviving the Last Great Time War which destroyed the Daleks as well as his own people, the Time Lords... including his last incarnation. I firmly believe that it is this last-of-his-kind status and emotional wounds that led him to form such a deep, and obvious romantic attachment to Rose Tyler.
That The Doctor was in love with her is undeniable, though he rarely expressed it in overt terms. He was the typical angsty college boyfriend in a sense, and had he lived he might have eventually overcome that aspect of himself. As it was, almost the last thing he did before dying was kiss Rose passionately in order to both absorb the Time Vortex to save her life and to say goodbye. It's one of those scenes you just live for if you're a Whovian.
And yet, he was also the most overtly bisexual of the modern three. He was obviously flattered immensely by the immediate attention he received from Captain Jack, and he flirted much more openly with him than he ever did with Rose. He doesn't react with jealousy toward Jack when he works his charms on Rose who reciprocates to the point of dazed infatuation. Instead, he stakes his claim to either of them should he see fit.
I would even go so far as to say that Nine was much more comfortable with Jack in a sexual sense than he seemed to be with Rose. Though he thought nothing of casually touching Rose, there was usually more heat when he interacted with Jack.Ten
Now The Tenth Doctor was as straight as time is not. He carried over his previous incarnation's torch for Rose, and their love story and ultimate parting makes the second series among the best in the whole run of the show. In addition to his growing acceptance of himself as a romantic partner for Rose, he also falls in love with another human, Joan Redfern, and is obviously affectionate towards Martha though he's too beaten up over losing Rose to reciprocate her feelings for him.
The thing is, he obviously wants to. That's the sadness of series three. The Doctor wishes he felt for Martha what she feels for him, and he knows he's hurting her. In the end, he strings her along because he loves her and needs her, but not in that way.
He also shows little or no interest in men at all. Unlike Nine, he is vaguely repulsed by Captain Jack, much to Jack's bitter disappointment. Granted, that has much to do with how "wrong" Jack is as an apparent immortal. Then, he gets hit on by Shakespeare himself. While amused and willing to play along for a joke, Ten is pretty obviously not interested. He is also the most willing to make gay jokes at other people's expense, something Nine and Eleven never did.
It's pretty conclusive that Ten at least was not anything but heterosexual.
Here comes the hard one. On the one hand, Eleven marries River Song (And Marilyn Monroe), and shamelessly flirts with her at every turn.
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On the other hand, I think it's safe to say that Eleven is not so much heterosexual and bloody clueless on how to go about any sexuality at all. I like to joke that the parts of his performance Matt Smith didn't life from Patrick Troughton he stole from Anthony Michael Hall in Sixteen Candles. That's an exaggeration, but it's more or less true.
Eleven tends to try and adhere to whatever sexual norms apply to wherever he is, but as he is arguably the worst TARDIS pilot since the First Doctor he usually gets even that wrong by not knowing where and when he is. You sort of get the impression that if he was expected to be gay at any specific place and time he'd go along with it without a second thought, but more of an act of custom than any real sexual desire on his part.
He tends to take a more weird Uncle approach to dealing with humans, as the Second Doctor did, and it's really only because he knows he ends up with River Song after the events of "Silence in the Library" that he seems at all capable of carrying on anything even remotely like a sexual relationship. Though it's clear that he desires to be thought of as handsome, winsome, and other omes, when it comes to actual sexual connection he lacks either Ten's firmness or Nine's flexibility.
He's the Morrissey of Doctor Who is what I'm getting at.