"You'd have to explain gay to him first. Then straight! Then why you were still talking when there's ALL THESE SPACESHIPS!! Then [he'd] be very cross it was ever in doubt, add a gay marriage setting to his screwdriver and accidentally marry a Krynoid. Again."
— Head writer Steven Moffat (when asked what the Doctor would think of gay marriage)
WARNING! THERE MAY BE UNMARKED SPOILERS!
"Doctor, look at the size of this Ho Yay page!" "Yes, Jamie, it is a big one."
(For the interested, you can read a blow-by-blow account (pun unintended) of every suspicious moment from almost the entire series and spinoffs (though the DW section stops with "The Waters of Mars") here.)
In "Terror of the Autons" (the Master's very first appearance), the Master isn't at all surprised that the Doctor survived his first two attempts to kill him, and refers to them as the opening salvos in their "game". This begins a trend apparent all throughout Roger Delgado's tenure, with the Master treating their constant battling as more of a friendly rivalry.
At the end of the episode, despite all the death and destruction the Doctor says he's "rather looking forward to" their next encounter, showing that the Master isn't the only one to enjoy it.
The Master caring for the Doctor in "The Mind of Evil", after the Keller machine nearly kills him, is straight out of a Hurt/Comfort Fic. Again this starts a trend in which while he continually tries to kill him, the Master always believes the Doctor will survive and doesn't actually want him gone.
"Colony in Space" has the Master offer the Doctor the opportunity to rule the entire cosmos... for seemingly no reason whatsoever, as he doesn't need the Doctor's help. After the Doctor (predictably) refuses, the Master becomes unreasonably angry, implying that he genuinely wanted the Doctor to rule side by side with him.
"The Sea Devils" has the Master admit that the only reason he keeps trying to destroy Earth is because it's the Doctor's favourite planet. This is part of yet another larger trend in which the Master deliberately targets Earth to infuriate the Doctor, much like a young boy pulling the hair of a girl they like because they don't know how else to express what they're feeling.
In "The Five Doctors", the Master openly states that "a cosmos without the Doctor scarcely bears thinking about", further supporting the idea that he never truly intends to kill the Doctor. He's genuinely nice to the Doctor throughout the entire episode, though the Doctor sadly doesn't believe him, and is very miffed when One doesn't recognise him from their Academy days (what with him having a new, stolen body).
In that same episode, the Third Doctor calls the Master "my best enemy".
On two separate occasions ("The Keeper of Traken" and the Made-for-TV Movie), the Master tries to steal the Doctor's body; he literally wants to be inside the Doctor. The former plays this very sexually, with the Master at one point toying with the ends of the Doctor's long curly hair, while the latter has this line "This body will soon decay. I NEED THE DOCTOR'S BODY!"
"The Sound of Drums" couldn't have stretched the subtext thinner, with a phone conversation that is, in between explaining how the Master survived the Time War, basically the Doctor trying to persuade the Master to have a long term relationship with him and the Master trying to get the Doctor to have phone sex with him. It's so strong that the Master needs to lampshade it, mockingly asking "Are you asking me out on a date?".
The (in)famous Say My Name bit, where the Master's reaction to hearing his name is closing his eyes and literally sighing with pleasure.
Master:Doctor. Doctor: Master. Master: I like it when you use my name.
The previous episode, "Utopia", has a similar exchange ("Use my name." "Master.") that wouldn't be out of place in a BDSM session.
"Last of the Time Lords" couldn't get more obvious if it tried. Particularly, the last ten minutes or so, what with the Master 'dying'in the Doctor's arms. And right before this, the Doctor reveals that the only safe place in the universe to keep the Master is... the TARDIS.
Doctor: The only safe place for him is the TARDIS. Master: You mean you're just gonna... keep me? Doctor: If that's what I have to do. It's time to change. Maybe, I've been wandering for too long. Now, I've got someone to care for.
During a bit of timey-wimey shenanigans, the Doctor's past self asks him:
Tenth Doctor: No, no beard this time. Well, a wife.
Russell T Davies, writer of all the Master's appearances in Tenth's era, called them 'practically soul mates' in a Radio Times interview.
"The End of Time" part one gives us the chase through the scrapyard, complete with piercing stares and heavy panting, the Master zapping the Doctor with his new electricity powers and the Doctor writhing in pain. And when the Master actually hits the Doctor, he stops attacking and runs over to make sure he's okay. The two reminisce about them playing in fields on Gallifrey as children, before the Master becomes rather insistent that the Doctor must understand him, taking it so far as to initiate a mindmeld.
Part two is, between the return of the Time Lords and the Doctor's angst about it and his impending death, almost entirely filled with Ho Yay goodness. Their back and forth banter while the Doctor is locked in what can only be described as a bondage chair, the Master taking the Doctor's favourite species and turning them into copies of himself (showing he's still jealous), the Doctor seriously contemplating whether killing the Master is worth saving everyone (which Wilf calls him out on), and the Master's final act being to sacrifice himself to save the Doctor. This exchange says it all:
Master: [shaking his head as his eyes fill with tears] Don't know what I'd be without that noise. Doctor: I wonder what I'd be without you. Master: [tearfully] Yeah.
When talking about the Doctor and Donna ("He loves playing with Earth girls!"), the Master is annoyed and bitter.
The Master, in a new android body, lives with the Doctor on the TARDIS in Scream of the Shalka. Paul Cornell later attended a Doctor/Master slash panel (as an audience member) and was asked about the relationship, and replied "I wouldn't be here if I didn't see it" and that in Shalka, the Doctor and the Master were "doing it". He later elaborated that he hadn't intended to write the story that way, but he adores the interpretation.
Their answering machine message was meant to imply a close friendship between the Doctor and his previous female companion. This was not even remotely clear in the finished product, and as such, it ends up sounding like the Doctor was recording while the Master was doing R-rated things to him.
"The Time Of The Doctor" gives us this lovely exchange (which Paul Cornell was downright giddy about):
Clara: I'm cooking Christmas dinner and I may have accidentally invented a boyfriend. Doctor: Yeah, I did that once, and there's no easy way to get rid of an android!
The Alex Macqueen incarnation of the Master, also in Big Finish, is by far the campest one of them all — while still being very, very sinister. His plans for Seven involve merging the both of them into a single being, with Seven's mind as a slave to his own, so they can rule the galaxy together for all of eternity. (He fails, of course.) When he finally meets Eight, he spends a few minutes simply admiring the Doctor's beauty, making appreciative noises and commenting on his hair.
Captain Jack Harkness exhibits rampant omnisexuality and a proclivity for flirting with anything that can say hi. He also kissed the Doctor before any of the other new companions did, and his spinoff show, Torchwood, is based entirely upon the premise that bisexual alien hunters are hot.
As for the Doctor, he's occasionally flirted right back at him.
Rose: Actually, Doctor, I thought Jack might like this dance.
The Doctor: I'm sure he would, Rose, I'm absolutely certain. But who with?
In the same episode, The Doctor utters perhaps the most suggestive line in DW history:
The Doctor: Welcome to the Tardis.
Jack: Much bigger on the inside.
The Doctor: You'd better be.
The Doctor continually curtailing of Jack's attempts to flirt with everyone they meet (male, female, or indeterminate) — allegedly because otherwise they'd never get anything done. It often sounds more like someone's just jealous.
The novel "Only Human", by queer author and gleeful shipping fanboy Gareth Roberts, spends much of its narration describing Jack in various states of undress. Including completely naked. As a distraction. And the Doctor, amused, comments that it's a nice distraction, but he's seen bigger... distractions.
The beginning of "Boom Town":
(Rose and Mickey are hugging.)
Jack: Aw, sweet, look at these two. How come I never get any of that?
During their conversation in "Utopia", the room full of deadly radiation was probably the only thing that kept one of them from jumping the other during that scene.
Jack makes little secret of the fact that he absolutely bloody adores the Doctor to the point of keeping his severed hand in a jar in Torchwood for two years, and reacting very emotionally when the container is threatened (and then shattered).
Jack: PUT IT DOWN! That's worthless to anyone but me!
And at the end of the first series season finale of Torchwood, when the hand (which is apparently functioning as Jack's Doctor-detector) starts glowing and we hear the sound of the TARDIS engines, Jack bolts so fast after the Doctor that Gwen, who was standing right next to him, doesn't even see him go.
After Jack realised that he Came Back Wrong, he spent the first few weeks getting extremely drunk, searching for the Doctor and yelling "I'M GOING TO KISS HIM, AND THEN I'M GOING TO KILL HIM."
During "The Sound of Drums" the Doctor explains a perception filter gadget he's making by saying "It's like when you fancy someone and they don't even know you exist." Behind his back Martha and Jack exchange looks:
During the teleconference sequence in "The Stolen Earth", Jack mentions knowing about Project Indigo, resulting in this little exchange between him and boyfriend Ianto:
Jack: I met a soldier in a bar.
Ianto: (aside) When was this?
Jack: (covers phone) Strictly professional.
Jack finally, properly, gets a sex scene in season 4 episode 3 of Torchwood. It's utterly magnificent and bordering on softcore porn. From the moment he grabs Brad's face and pushes him to his knees, to the quite sudden role reversal and Jack getting pounded hard — it's everything the fans had been wanting to see for years. And since he's not invincible that day (long story), he insists on using condoms.
Ten's very final parting gift to Jack: playing wingman to hook him up with Alonso.
Eleven absolutely doesn't care about social norms or nudity taboos, has No Sense of Personal Space, and generally brings to television all the lovely things Eight was only allowed to do in the novels. He's also the first incarnation since Eight to randomly kiss companions when he gets excited, without needing some kind of excuse for it.
Eleven and Rory have a bit of this going on from the moment they meet, mainly thanks to Eleven's complete disregard for personal space and their Foe Yay-filled rivalry caused by Amy. It's hilariously one-sided due to Rory's Single-Target Sexuality.
There is a cut scene from "The Hungry Earth" where Eleven gets distracted wondering where Rory is, before stating almost dreamily that "I like him. A lot." It's adorable and most definitely should have been left in.
And then in "Cold Blood" Rory dies to save Eleven. Which is followed by Eleven telling Amy to remember "funny, gorgeous Rory".
Also, at one point the Dream Lord sends the Doctor and Rory back into the alternate reality together, offering to "keep" Amy and let the Doctor have Rory all to himself... for all eternity. Rory and the Doctor then proceed to fall asleep entangled together on the floor of the TARDIS.
Speaking of Eleven's personal space issues, Rory is definitely the most frequent recipient of Doc's hello face-touches.
During a scene in "Day of the Moon" when they've all faked their deaths to get into Area 51 and are taken into the Doctor's prison via bodybags, it's Rory who the Doctor goes for straight away and you can see him kissing his forehead to one side of the screen.
In "A Good Man Goes To War", when Amy and Rory are finally reunited with Melody, they start crying and making out just as the Doctor walks in. He is hastily trying to excuse himself when Rory points his sword at him and demands he come back.
The Doctor grabs Rory's head and kisses him full on the mouth in "Dinosaurs On A Spaceship". Just because he feels like it. Amy doesn't seem to mind. (Rory makes a "yuck" face.)
As was revealed during the 2013 Gallifrey One convention, the snog wasn't actually in the script. Matt Smith just likes kissing people.
They previously shared a kiss in the comics, after the Doctor and Amy accidentally switched bodies. Rory doesn't even care that Amy has a different body and kisses her to reassure her... until he realises that they've already switched back to normal, and he just accidentally kissed the Doctor. (Amy asks them to do it again. Slower.)
In "The Power of Three", the Doctor looks very happily at Rory in his underpants. Rory also kisses the Doctor on the cheek in the episode. Just casually. Eleven makes a very happy "oooh!" sound.
The very first episode of Eleven's tenure has him borrowing a hunky guy's laptop, and later in the episode he refers to him as "Amy's friend... the good-looking one". It helps that Jeff seems perfectly happy to let the Doctor get all in his personal space. In fact, cut dialog from that scene even has Jeff's grandmother asking (of the Doctor) "Jeff, is he your gay friend?" despite protests from Jeff that he isn't gay.
In that same episode, Eleven kept running an appreciative eye over Bill Nighy as a museum curator because he likes his bow ties.
"The Lodger" is pretty much a mass of Ho Yay directed at Craig. Eleven strokes him constantly, displays a complete disregard for his personal space and grabbed him at at least one point (although that was for the purposes of telepathy). The Ho Yay of this episode peaked with Eleven stroking Craig's face when he was poisoned and incapacitated, and tenderly saying "You're important". Not to mention Eleven's lack of hesitation in approaching both Craig and Sophie while wearing only a towel.
Absolutely off the charts in "Closing Time"; the Doctor plus Craig plus a baby adds up to make the episode one long, unbroken Mistaken for Gay sequence, and that's not counting the bit where the Doctor attempts to distract Craig from the approaching Cybermen by declaring his passionate love for him and attempting to kiss him to prove it. Craig's only objection, by the way, is that he is already in a relationship.
"I danced with everyone at their wedding. The women were all brilliant. The men... were a bit shy."
He considers the founding fathers of the United States "lovely fellas. Two of them fancied me."
He's friends with Franz Schubert (who was Ambiguously Bi), and happily babbles about how "Franz the Hands" likes to tickle him while they play the piano together.
In "The Snowmen", Eleven goofs around with a Punch handpuppet and snogs it. It proceeds to hit him in the face, not entirely unlike how his relationships typically pan out.
In "Cold War", Eleven tells David Warner"I could kiss you!". Warner's character isn't all too bothered by the idea, since kissing on the mouth was a common gesture of friendship between men in the Soviet era. Eleven looks mildly confused and decides on "later!".
Eleven and Professor Brian Cox have some of the most intense Ho Yay in the series so far, in the special "The Science of Doctor Who".
Eighth Doctor and Fitz
Where to begin with Fitz Kreiner and the Eighth Doctor from the Eighth Doctor Adventures... Over the course of their fifty-something books together, they become Not-So-Heterosexual Life-Partners. EDAs can be divided up into "Fitz and the Doctor are rather gay for each other" books and "Fitz and the Doctor are really gay for each other" books. This is all massively confusing for Fitz, who identifies as straight and has a number of issues with suddenly being in love with an alien bloke. A few examples:
The Doctor happily kisses Fitz on the mouth and "delicately" on the hand, and after spending much of a book looking up and down for him, the Doctor learns Fitz is alive through a video link and kisses the screen in happiness.
In the same book, Fitz has managed to both sprain and get a shotgun wound in one of his legs. When the group has to make a fast getaway, the Doctor carries Fitz bridal style to safety. The author thought it was important for everyone to know how "almost romantic" it was.
Fitz outright admits, via internal monologue, to wanting to "get laid by" the Doctor. When someone uses mind control to make Fitz love her in another book, Fitz breaks out of it by saying, "I've been engineered to love you, Carmodi. With the Doctor - it's the real thing." At one point, the prospect that they may not be able to use the TARDIS comes up and Fitz wonders if they'll end up settling down together in "that house [the Doctor] had in Kent and grow roses."
While the Doctor is alone on Earth for 100 years, he's obsessed with a song he can only half-remember. "Do you know, I've had a tune going round and round in my head for more than a hundred years. I don’t have the slightest idea what it is. I want to know." It's revealed to the reader at the very end of the book this song is Fitz's, one he wrote for the Doctor. So the Doctor forgot everything about himself, the Time Lords, Gallifrey, but he remembered a song Fitz wrote for him.
When the Doctor manages to lose Fitz, he does some very shady things to get him back, including talking the clone-of-a-clone-of-a-clone of Fitz, a kid named Kode, into suicide so he can basically reprogram Fitz into Kode's body. The fact that he lies about it to his other companion implies the Doctor knows how sketchy it was.
The Doctor, generally Oblivious to Love, actually flirts with Fitz ("I'll show you my tattoo if you're lucky."). Fitz also seems to be the only companion in the EDAs whose physical appearance the Doctor really notices, and he compliments Fitz when he's looking uncharacteristically well-groomed.
After spending an entire book having a massive Heroic BSOD, Fitz pulls himself out of it by explicitly making his new purpose in life looking after the amnesiac Doctor.
Fitz is said to "dote on the Doctor", makes him three meals a day with little notes when he's locked up in his room mourning, and is the target of serious worry from the Doctor sometimes when they are apart.
The very last line of Parallel 59, which follows the Doctor being joyfully reunited with Fitz and then watching Fitz be reunited with his Girl of the Week, strongly implies that what the Doctor feels for Fitz is love in some sense.
He whistled as he walked, Fitz’s plaintive little melody still in his head. Thinking of loved ones, coming home.
There is much more, to the point no fan would be surprised if one of the EDAs ended with, "And then the Doctor and Fitz went back to the TARDIS and shagged." To see more examples, check here and here.
And last but not least, their first meeting is rife with meaning. Fitz is working in a plant shop, lamenting how his life is being wasted away, when the Doctor shows up and tries to purchase a very symbolic flower.
"I'd like to buy this begonia."
"This begonia? But it's nearly dead."
"I know. I intend to rescue it."
27 books later, he still has that begonia. As well as Fitz.
In the Big Finish printed story "The Feast of Seven... Eight (and Nine)" by Vanessa Bishop, from Short Trips: A Christmas Treasure, Eight celebrates Christmas by... grabbing some mistletoe and trying to make out with all his former selves. He succeeds with Five and Three. And dreamily sighs about Puccini having such soft lips. And Seven gets offended by the whole thing and tells Eight that Six is "more that way inclined".
Ace gets suspiciously chummy with a female guest cast member in almost every story. We really have to give special mentions to:
With Mel in "Dragonfire". Especially when her first response to Mel falling over and being knocked out is to do what is probably meant to be feeling for a skull fracture, but looks more like stroking her hair. It's more blatant in the novelisation, where Ace and Mel descend an ice face using mountain climbing gear rather than the pack ladder used in the serial and this exchange takes place:
'I've never done this before,' admitted Mel. 'You must have done it lots of times.' ‘Well, not lots of times…’ Ace was avoiding Mel’s eyes. ‘How many times?’ asked Mel suspiciously. ‘This’ll be the first.’ Ace looked up guiltily. ‘But I’ve seen them do it on telly, and it’s easy!’ Mel looked at Ace. The safety harness Ace was wearing didn’t look quite right. ‘I think you’ve got that harness on upside-down. I think those tight straps are supposed to go between your legs.’ Ace looked down, and giggled. ‘It’s a good job I’m not a boy!’ she laughed. Mel smiled - and then she began to laugh as well. This wasn’t going to be a bit like they always showed it on telly!
With Shou Yuing in "Battlefield". They bond over a shared love of explosives and at one point are huddled inside a chalk circle clutching a sword.
In "The Happiness Patrol" with the repentant Patrol member Susan Q, who talks to her about being closetedly sad. In the deleted scenes package on the DVD, Susan Q tells Ace "As long as you're looking cute we've got a chance".
Jean and Phyllis in "The Curse of Fenric", who also seem rather determined to get Ace to join them early on, and after they become Haemovores they tell her, "You should have come into the water with us. Then we'd have been together." This is another case where the novelisation goes a bit... deeper with things. Not only is there implied to be a past relationship between Millington and Judson as mentioned below, but it's pretty clear in the book that Jean and Phyllis were probably a couple as well, even before their transformation.
Ace definitely had a thing for Kathleen in "Curse of Fenric". Absolutely no sense of personal space, she's constantly taking time (when they really don't have much to spare) to run off and check on her and the baby... She even refuses to accompany the Doctor into a fight because she wants to stay and take care of them. Keep in mind that this is Ace McShane, who normally refuses to be left behind, hates "dark buildings", and loves a good fight more than anything, turning down the Doctor's request for help in order to barricade herself into a barracks with a sweet, gorgeous, intelligent recently-widowed army wife. Who happens to be her grandmother. And whom she promptly risks her life for to help her escape to London—sending them to her own family, no less.
Tegan and Nyssa
The TARDIS is infinite, and yet Nyssa and Tegan share a very cozy room and not only never question this arrangement, they seem to be pleased as punch about the whole thing. For context, the only other people who have shared a room in the show's history are canon couples Ian and Barbara (confirmed to have finally gotten married in the SJA) and Amy and Rory.
Nyssa and Tegan hit it off quite well from the very beginning, with Tegan being the more likely to stand up to pushy individuals and Nyssa acting as the voice of reason. This includes their original meeting, where Tegan goes from visibly upset to happy upon seeing Nyssa, at that point a complete stranger.
Nyssa's gentle fretting and care for Tegan in "Snakedance" edges a great deal past mere friendly concern.
Nyssa is deeply upset when the Doctor leaves Tegan behind without warning in "Time-Flight", insisting they shouldn't have just left her.
In "The Arc of Infinity" Nyssa's priorities pull a 180 from worrying about the Doctor to wanting to hear every detail about Tegan the moment they hear from her. She's very quick to pull Tegan firmly back onto the team when she turns up again, and nearly throws a fit when the Doctor is about to venture into the Matrix to find Omega's location from Tegan, on the grounds that she might be killed. The next time she sees the Doctor, she won't even look at him until he tells her Tegan is all right.
"Black Orchid" has this in spades. Tegan cheerfully demonstrates the Charleston for Nyssa. Tegan can tell Ann and Nyssa apart and is insufferably smug about this. (Context: In a discussion between Ann and Nyssa we learn that the only visible difference is a mole on Nyssa's back, which isn't visible even in a relatively low-cut butterfly dress.) Upon the reveal of their twin act:
Muir: I might have known they were up to something. Now no one can tell them apart. Tegan: I can. Muir: How? Tegan:[smirk] That's a secret.
"Mawdryn Undead" is basically Nyssa and Tegan being married while trying to keep an eye on a bumbling, overgrown alien schoolboy (and Turlough). When not-actually-the-Doctor tries to order Nyssa to dematerialize without Tegan (again), she only argues for a minute... and then walks defiantly out of the TARDIS. The scene where Tegan goes for help is difficult to read as anything but a worried couple hovering over their injured kid and not knowing what to do, with Nyssa's fretting as she tells Tegan to be careful and to take the TARDIS communicator. For that matter, Tegan's very real fear when she realizes she just left her best friend alone with a stranger who probably isn't the Doctor, upon which she runs back to the TARDIS. The sheer relief in her voice when she finds Nyssa safe and waiting for them...
Doctor: It'll be good to see the TARDIS again. Nyssa: And Tegan!
Despite knowing the Doctor longer and having spent more time with him—all those adventures while Tegan was on Earth—Nyssa is able to remain calm and collected while saying goodbye to him, asking him politely not to be upset and to let her leave in good faith, to part as friends. Then she has to say goodbye to Tegan and breaks down sobbing into her chest.
Tegan's horrified head-shaking in the background when Nyssa tries to tell her that she's chosen to stay on Terminus, and her desperation when she asks the Doctor not to let Nyssa stay on Terminus to die, and her growing realization that Nyssa's really not coming with them. By the time Nyssa asks them to stop trying to convince her so they can part as friends, loud angry defiant Tegan Jovanka can barely manage to whisper "...Please, Nyssa...?" And of course, their tearful goodbye.
Tegan: She'll die here. Nyssa:[voice breaking] Not easily, Tegan. Like you, I'm indestructible.
In the Big Finish adventure "Cradle of the Snake":
Within the first seven minutes, Tegan (admittedly Tegan possessed, but still) has Nyssa pinned against the wall purring about how much they'll enjoy themselves if Nyssa stays. Several times it's mentioned that the influence of the Mara works by forcing people's dark sides and subconscious desires to the surface. Throughout the audio and for no reason whatsoever except for its long stay in Tegan's subconscious, the Mara has a sexually-charged obsession with Nyssa. It sneers about her purity and calls her "little nun", implying that her rejection of its advances actually offended it, and while possessed not only can none of the Mara's minions take their eyes off Nyssa, but the Mara's influence on her involves her dressing scantily and in black.
Nyssa opens the audio by gently shooing Turlough and the Doctor away so she can take care of Tegan on her own. Tegan—who'd locked herself in their room and had refused to open the door for what appeared to be a long period of cajoling by the Doctor—instantly lets Nyssa in when she's asked. One of the first things Nyssa says is that Tegan's been sleeping badly and having nightmares again, to which Tegan's reply is a tired "Sorry to keep you awake." (Admittedly they do share a room, but if they slept on opposite sides of the room it's very unlikely that Nyssa would be woken up by Tegan's restless sleep unless she actually woke up screaming, which doesn't appear to be the case, so it's logical to conclude they're sharing a bed.)
Even while under the influence of the Mara after it gives the explicit order that Tegan and Turlough are to be killed on sight, Nyssa goes out of her way to hide Tegan and keep her out of the way of the other members of the Mara's council, to keep her safe. She even consoles Tegan—sort of—about the fact that the Mara rejected the idea of possessing her again, explaining that some people just aren't born to power, and then makes her a very interesting deal...
"But I tell you what. If you work hard, I'll let you be my... personal assistant. Would you like that?" (Yes, that pause is in the actual audio.)
Writers Paul Cornell, Gareth Roberts, Russell T Davies and Steven Moffat all merrily ship the Doctor with guys, and have all explicitly stated that the innuendo is very much on purpose. Current show-runner Moffat is of the opinion that the Doctor has been flirty with his male and female companions since ever, and that the Doctor, in fact, can't be bothered with silly human concepts of "gay" and "straight". He's also the guy who invented Captain Jack Harkness, and has casually stated that River Song was probably involved with her entire archaeology crew.
Leela and Romana seemed to get interestingly chummy with the female guest stars.
And then Leela and Romana became co-stars in the Gallifrey audio series. Romana takes an entire week out of her schedule as the President of Gallifrey, with no warning, specifically to take Leela to a spa planet and talk about their relationship. They proceed to talk about Romana's regenerations in the context of reassuring Leela that unlike her husband, Romana will never leave her.
Leela: I was so alone in the world of dreams when you left... the wild lands were dark, and so quiet... I... I do not wish to be alone. Romana: There will be a place for you with me, always. Whatever face I wear.
In "The Robots of Death", Toos seems unusually attached to Leela, to the point that she requested Leela check on her arm again even after a robot offered to take her to Sickbay. Toos then proceeds to have a nice elaborate Security Cling with Leela on her bed, surreptitiously groping her naked thigh.
Donna picks up where Leela and Romana left off in the "getting chummy with female guest stars" category, namely Evelina in "The Fires of Pompeii", Martha and Rose in their guest appearances, Jenny in "The Doctor's Daughter", and flipping Agatha Christie in "The Unicorn and the Wasp". Special mention goes to Miss Evangelista in "Silence in the Library"/"Forest of the Dead", to the point that her dying request is to speak to Donna, and she deliberately seeks Donna out in CAL's simulated world.
A memorable moment between Shakespeare and the Tenth Doctor in "The Shakespeare Code" (keep in mind the real Shakespeare is widely speculated to have been bisexual):
Doctor: Come on, we can all have a good flirt later! Shakespeare: Is that a promise, Doctor? Doctor: Oh, fifty-seven academics just punched the air.
This exchange in "Daleks In Manhattan":
Martha: I'm so glad to see you! Tenth Doctor: Yeah, well you can kiss me later. You too Frank, if you want.
The Second Doctor and Jamie. Getting◊ all◊ up◊ in◊ each◊ other's◊ personal◊ space,◊ oh◊ yes.◊ They hug constantly, they flirt, they banter like an old married couple, and of all the companion/Doctor relationships, they seem most like a dynamic duo rather than "the extraordinary Doctor and his amazed companion along for the ride". The actors were very close friends, and Frazer Hines commented that he could read Troughton's mind just by looking into "those twinkling eyes", and that much of their thoughts of spending time with each other sadly had to remain "private".
Not just constant hugging, but constant touching — they epitomizeNo Sense of Personal Space. Jamie is a master of the Security Cling and, while he'll grab onto his co-companions or random one-off characters who happen to be nearby, clings to the Doctor with truly ridiculous frequency.
That moment when the Doctor fondles Jamie's sporran, and a scene which only survives in telesnaps but which depicts Jamie on the Doctor's shoulders — and the Doctor rather definitely looking up.
In "The Evil of the Daleks", when the Doctor has to manipulate Jamie as part of a plot and Jamie finds out, he tells the Doctor "We're finished!" and refuses to touch him. (It doesn't last long.) And the sheer terror on the Doctor's face when he finds out that the Daleks want to use Jamie in their experiments. Not until the Revival series would a Doctor go into a similiar panic at the thought of a companion being harmed.
Turlough. There certainly seems to be some mutual crushing going on in "Mawdryn Undead", Turlough's first episode; it would also explain the Doctor's otherwise inexplicable decision to trust Turlough after Turlough has introduced himself by trying to steal the TARDIS. There's also this line, from the commentary, on the subject of why the Doctor trusts him so easily:
Malcolm? Hero-worship is understandable, but running up to the Doctor, hugging him very tightly, and saying "I love you!" over and over is a bit different.
The increasingly Ho Yay interactions between Max Stael and Adam Colby in "Image of the Fendahl", which escalates to Adam being tied to a column with three buttons of his shirt unbuttoned and Max stroking his face with a pistol. Scott Fredericks has stated he deliberately played Max as bisexual.
Mr. Finch from "School Reunion" softly asking the Doctor to rule the universe at his side to a background of piano music comes to mind.
In "Rise of the Cybermen"/"Age of Steel" there was Rickey/Alternate Mickey and his boyfriend Jake. The actual expository scene was cut for one reason or another, making their canon relationship into simply oodles of hoyay.
In "The Vampires of Venice" we get lots of Les Yay from Signora Calvierri, who is basically a dominatrix-y older woman surrounded by sexy younger women who she regularly drinks blood from. (At one point this included Amy.)
Adric has huge Ho Yay with both Four AND Five. Lots of longing glances, and thoroughly unnecessary compliments of the Doctor, such as one bit where he says something along the lines of "Oh, Doctor, your handwriting is just lovely", in this really quite suggestive way. Not to mention his persistent daddy issues with just about any powerful male figure the team encounters, evil or not. (Not really relevant, but his actor Matthew Waterhouse is gay.)
In the 2011 Comic Relief Red Nose Day mini episode "Time": Amy Pond and Amy Pond.
Amy: Mmm... I'd give you a driving licence. Amy: I'll bet you would. The Doctor: Oh, this is how it all ends. Pond, flirting with herself. True love at last. [remembers that Amy's husband is also present] Oh, sorry Rory. Rory: [nearly catatonic] ...absolutely no problem at all...
Madame Vastra and her chambermaid Jenny from "A Good Man Goes To War" do not qualify simply because it's definitely not subtext. It's canon as of "The Snowmen", where Vastra introduces Jenny as her wife.
Also in "The Snowmen", Vastra is definitely hitting on Clara while "testing" her. Jenny doesn't seem to mind.
In "The Invasion", Isobel is quite clear that she only wants to photograph Zoe, not Jamie. And then she gets Zoe to wear a miniskirt, and photographs her from floor level.
There is a definite, if subtle, romantic undertone to Rumford and Fay's relationship in "The Stones of Blood". Mary Tamm herself said "We were all so innocent back then" when the Les Yay was pointed out to her.
"The Curse of Fenric":
Two of the only survivors of the serial are a British soldier and a Russian soldier who decide there isn't any point to fighting anymore, and who are last seen with their arms wrapped around each other with big grins on their faces.
The novelisation heavily implies a homosexual relationship in the backstory of both Millington and Judson, and their sourness towards each other is in part because it ended very badly.
When Jean and Phyllis tell Miss Hardaker that they're going to Maidens' Point (they had agreed to meet Ace there), she gets angry and says, "I know what girls who go to Maidens' Point have in mind!" You expect her to follow this up with something like "You're going there to meet with boys!" But no, boys aren't mentioned at all in this little lecture; just "girls with evil in their hearts".
Why was Ping-Cho in "Marco Polo" so anxious for Susan to say "goodbye" to her?
In "Daleks in Manhattan", Martha seems way too excited to watch Tallulah's dance number.
"The Happiness Patrol" is loaded with Ho Yay to the point that there's a serious argument that the whole thing is a deliberate queer rights allegory. As well as Ace's friendship with Susan Q (mentioned above), the dysfunctional relationship between Gilbert M and the Kandyman really is like a married couple turned sour, and of course Gilbert M and Joseph C run away together at the end. In the deleted scenes, Gilbert M's reaction to the Kandyman's death is "There's nothing here for me now.", at which point, Joseph C makes a suggestion...
At the end of "The Daemons", everyone merrily joins in the Dance Party Ending and the local witch makes sure to point out that it's a fertility dance. Hearing that, Captain Yates asks the Brigadier: "Fancy a dance, sir?" ("Kind of you Captain... I think I'd rather have a pint.") The "Making of" segment of the DVD has Nicholas Courtney pretty much confirm (as quoted by Katy Manning) what we were already thinking — "The Brig's an alcoholic and Mike Yates is gay!". According to the Doctor Who New Adventures, Mike eventually ends up with a guy.
The Doctor's friendship with the Corsair has serious Ho Yay overtones. According to Neil Gaiman, (s)he and the Doctor occasionally woke up in cells together after bouts of heavy drinking. (And once in the vault of the Bank of England.)
"Fantastic bloke. He had that snake as a tattoo in every regeneration. Didn't feel like himself unless he had that tattoo. Or herself, a couple of times. Oo-hoo! She was a bad girl!"
Giuliano and Marco in "The Masque Of Mandragora" are beyond blatant, with Undying Loyalty on both ends. Giuliano trusts Marco enough to confide in him unquestioningly despite his uncle's spies being everywhere, while Marco is so devoted to the Count he'll willingly endure Medieval-style torture rather than betray him.
In "The Ghosts Of N-Space", the Doctor fondly recalls how he and his old teacher used to go skinny dipping on Gallifrey. (And earlier in the episode, Sarah Jane — posing as a page boy — gets mistaken for the Doctor's catamite.)
As the Great Intelligence, Richard E. Grant grabs the Doctor's face with a black leather glove and brings their mouths close together while they stare defiantly at each other.
As The Discontinuity Guide points out, there's only one bed in Izlyr and Ssorg's room in "The Curse of Peladon".
Doctor Who Magazine comic companions Izzy and Fey share a bit of flirtation, a lot of adventures, and — once Izzy manages to overcome her fear and be open about her sexuality — a nice proper snog.
Izzy and Destrii blatantly flirt with each other when they first meet, with Destrii calling her new friend "Sweetie" and commenting on her body a lot, and Izzy just making cute faces and happily jumping on Destrii's back at the first opportunity. Too bad Destrii reveals herself to be evil and ends up taking Izzy's body, but not in that way.
There's a distinct undercurrent of something between Majenta Pryce and her sometime-cellmate Zephyr (with Majenta deciding to take Zephyr along in the TARDIS, which ends up getting nixed by the plot), and the end of Majenta's arc sees the two of them heading off together to seek their fortune. Amusingly, emails between RTD and the magazine staff included the stipulation "No more lesbians" — either he wasn't actually serious, or they figured bi women were still fair game.
The implications of Rose ending up with the clone Doctor in the end of "The Stolen Earth"/"Journey's End", and the clone Doctor saying something to her that we didn't hear ends with them kissing. For the Doctor to properly return Rose's love, and say what she needed to hear, he had to be part human. Specifically, part Donna.
Word Of Moffat says Tasha Lem and Madame Kovarian were married, before the whole Trenzalore thing caused the schism in the Church.