Hugh Laurie agreed when an interviewer called Wilson "the other love of [House's] life". He also famously said he can easily see House getting it on with Cuddy, Cameron, or Wilson. Katie Jacobs, executive producer of House, once implied this too.
A story arc from the end of Season 4 implies that Wilson is dating Amber because of her similarity to House. House calls him on this in "Don't Ever Change".
In discussing Amber's assertive qualities:
Wilson: She has an annoying quality. Perhaps even two. If I was perfect, I would date perfect.
House: You like that.
Wilson: It's annoying, but she's good at it.
House: Wait a second. This isn't just about the sex. You like her personality. You like that she's conniving. You like that she has no regard for consequences. You like that she can humiliate someone if it serves (Beat) Oh my God. You're sleeping with me.
Later:
Wilson: House, you're right. Why not? Why not date you? It's brilliant. We've known each other for years. We've put up with all kinds of crap from each other. And we keep coming back. We're a couple.
House: Are we still speaking metaphorically?
That same scene finishes with House giving Wilson a very serious glare (indicating that he'd touched a nerve), which Wilson brushes off with a flippant, "Well, if you'd looked at me with those flashing eyes before I was involved..."
In "Hunting", a gay patient of House's mistook him and Wilson for a couple, causing Wilson to stammer nervously.
In "The Mistake", House stated (albeit sarcastically) "I'm gay", citing his closeness with Wilson and "obsession with sneakers."
In "Clueless", House kicks Wilson out of his apartment after letting him spend the night:
Wilson: You're kicking me out? After one night?
House: You think we should try counseling first? Why d'you want to sleep on a couch, anyway? You've got money. At least until the divorce is finalized.
In "Failure to Communicate" House calls Wilson and greets him with "Hey honey, how are the kids?" (referring to his team. Which Wilson actually is keeping tabs on while House is away.)
In another episode, House declares "I love you" when Wilson gives him more Vicodin in "97 Seconds", causing Squee in millions of Ho Yay fans.
House can sometimes act like something of a Stalker with a Crush towards Wilson, sort of. The crush part is up for debate, though. In the beginning of Season 5, House hires Lucas to spy on Wilson when Wilson cuts ties with House, quits his job, and moves away. Lucas accuses House of wanting to see if Wilson is pining, and he's right. House is clearly upset to discover that, despite having Lucas set up bugs and everything in Wilson's car and home, Wilson hasn't mentioned House at all.
"Birthmarks", the fourth episode of season five, is supposed to focus on the funeral for House's father. Instead, it bounces between how they first met to getting House and Wilson back together.
Also worth noting that while it's first suggested that House's mother called Cuddy, in reality she called Wilson to get her son to the funeral.
Then there's this:
House: If you're coming back because you're attracted to the shine of my neediness... I'd be okay with that.
"Under My Skin". House is picking a fight with Wilson, and hallucinatory Amber cuts in with "Stop deflecting. He cares about you. You care about him. Tell him you love him." When you consider that Amber is a manifestation of House's subconscious...
In Season 5's "House Divided", House wonders if he's hallucinating Amber, Wilson's ex, as his anima out of "some secret and very unconscious desire to get Wilson into my bedroom". There is no clue in his sleep-deprived tone to how sincere or not he's being.
The end of "Both Sides Now", when scenes of Chase and Cameron getting married are intercut with scenes of Wilson taking House to the psychiatric hospital. It's essentially a scene where one couple comes together and another is being torn apart.
In the season 6 episode "Brave Heart", Wilson walks in on House masturbating. What makes this situation peculiar is the fact that it's bright and early, House is in Wilson's living room on his couch, and Wilson's entrance into the room is not subtle. It also doesn't help that, upon being caught, House makes a masturbation joke (much to Wilson's disgust), launches into a conversation about their living arrangement, and smiles after Wilson leaves. It's quite possible that House actually wanted Wilson to catch him.
It's rather telling that, on the occasion when House was planning on crashing Cuddy's Thanksgiving dinner with the professed intention of breaking her and Lucas up in "Ignorance is Bliss", he couldn't resist asking Wilson to come with him... "as [his] date".
House spent an inordinate amount of time rambling to his team about his and Wilson's relationship in season 6's "Remorse", concluding with the smugly definitive statement "And that is why he will never mate me!", prompting a long, awkward, silence and great reaction shot from the fellows. House then attempted to clarify by insisting "It's a chess term," leaving them looking thoroughly unconvinced.
In "The Down Low", Wilson is frustrated because a woman he is interested in is convinced that he's dating House.
Wilson: Everyone in our building thinks we're gay.
House: We're grown men over the age of thirty who moved in together. We're two tigers away from an act in Vegas.
The episode's whole B-plot is House pretending that he & Wilson are a couple so that Wilson can't sleep with her. After trying and failing to convince her that they're both straight, Wilson proposes to House in a crowded restaurant to make him drop the act.
House: What are culottes anyway?
Wilson:(minutes after denying he was anything less than straight) Pants that hang like a skirt. (Realizes how incredibly gay that sounds, annoyedly waves House's comments off.)
From season 6, "Private Lives":
Wilson: What are you doing?
House: Masturbating. I'd invite you, but people are already talking.
Also, the look House gives Wilson when the porno music comes on over the speakers.
In the episode "Black Hole" from season 6, House forces Wilson to buy a piece of furniture that says something about him: Wilson chooses an organ that House absolutely loves. House's response is, "I like what this says about you." To elaborate, in previous episodes Wilson got mad with Cuddy for hurting House and outbid her on the loft she was trying to buy. Then he moved in with House. House spent the entire episode pestering Wilson about furniture, going so far as to saying that if Wilson is incapable of buying furniture for himself, he's empty inside. Cue Wilson nearly driving himself crazy trying to buy furniture and failing miserably; finally, he gives in and uses an interior decorator. The only thing in the whole apartment that Wilson actually manages to choose and buy on his own is an organ, which isn't even for him, but explicitly intended for House. Implications are clear: House is the only fixed point in Wilson's life, the only thing Wilson's absolutely adamantly sure about, and he chooses to honour that. Frankly, this may be the most romantic gesture anyone on this show has made to anyone.
In "Baggage", House describes Wilson as a consolation prize in lieu of Cuddy, and his story about her instead focuses on Wilson.
In the season 7 premiere "Now What?", House and Cuddy had just finished having sex, leading to this exchange which just screams OT3.
Cuddy: Why didn't you let him in?
House: You were thinking about Wilson while we were having sex? That's so cool, so was I!
The entirety of the House/Wilson subplot in season 7's "Unplanned Parenthood" is rife with this. For the purposes of this episode, House and Wilson are Rachel's dads. When problems occur with Rachel, what does House do? Does he tell Cuddy, the child's own mother? No; he immediately confides in Wilson and they spend the rest of the episode trying to hide it from her and take care of Rachel. Not to mention House's line that Wilson would be a "great 'mommy'".
In hindsight, while shitty for the House/Cuddy friendship, she tells him he'll always put himself first and that's why she can't be with him. In the finale, when Wilson doesn't have long to live (and he'll almost certainly be alone and have nothing when that happens)? He fakes his death and destroys his entire career for him.
In "Larger than Life", House tells Cuddy that he doesn't want to go bowling with Wilson because his chances of sex with him are "considerably lower" than with her, implying that sex with Wilson is both possible and not unwanted.
From "Out of the Chute"
Carnell: Don't worry. You can trust me with anything. Including your food.
House:(indicating Wilson) After he and I have sex, I'm going to slit his throat and then disembowel him in the bathtub.
In "Transplant", House spends the entire episode trying to get Wilson back. He tries a risky revival method on the lungs for Wilson. He misses the sound of his voice. They have a song - and it's "My Heart Will Go On." House likes Wilson, he has fun with Wilson. He finds a vegetarian restaraunt for him. They go to dinner. House is willing to get hurt for their friendship. It's basically Ho Yay: The Episode.
House: I like you. I have fun with you. And, if you can honestly say that you don’t like me, you don’t have fun with me, I can accept that. But just do whatever you have to do to get over this. Punch me in the face, kick me in the nuts. Either/or. Both seems excessive.
Wilson: The thing is, House… I don’t like you. *leaves*
House:*looks broken hearted*
As of "The Confession", House now has a part of his wall movable (he presses a button on a remote, it moves) and it opens to show Wilson's office. Aww.
Season eight's "Better Half" gives us this gem.
House:(to Wilson) I really gotta get you laid. If I have to plough that furrow myself, so be it.
This conversation from House and Wilson in "Man of the House" needs no explanation:
House: Need my apartment key back.
Wilson: If you're breaking up with me, can we at least talk about it first?
House: Maybe if you weren't all nag and no shag.
Wilson: I don't sleep with married men.
Season eight's "The C-word" cements it forever and ever. When Wilson finds out he has cancer, House goes on a vacation and helps him carry out an incredibly dangerous, completely nightmarish, potentially lethal and most likely illegal chemotherapy. In House's flat. House holds the bucket when Wilson's throwing up; House goes without Vicodin so he can give it to Wilson; and when Wilson's half mad with pain and screaming abuse at House, House holds his tongue. And it turned out he made a truly hilarious video of the whole terrible experience, which made Wilson laugh like he probably hasn't laughed for weeks. If that's not true love, then I don't know what is.
Wilson: If things go wrong, I just want you to know—
House: If you're gonna say that you've always been secretly gay for me, (Beat) everyone always just kind of assumed it.
From the same episode, when House walks into Wilson's office:
Wilson: Go away, I have a headache.
House: We don't have to have sex. Sometimes it's nice just to cuddle and talk.
In "Post Mortem":
Wilson: I want a threesome.
House: Shouldn't we try a twosome first?
This line, including the little smiles they exchange afterwards:
The penultimate episode of the show, "Holding On", contains more Ho Yay than all the previous seasons put together. In addition to House almost killing a patient out of despair because Wilson's refusing further chemotherapy, we have House telling Wilson that he needs him and doesn't know what he'll do without him, Wilson asking House to tell him that he loves him and the two of them planning how they're going to spend the next five months until Wilson's death.
Wilson: Just dinner?
House: Depends on how much we have to drink.
House tells Wilson he's the only one House listens to, and that Wilson is smarter than him. Coming from Mr. "all I have is my brain", that's huge.
And Foreman finally expresses the beauty of House's and Wilson's friendship: they are the most lasting relationship any of them has ever had. Screw having sex: these two are in love.
In the series finale "Everybody Dies", House fakes his own death and gives up everything else in his life to be with Wilson for the 5 months until Wilson dies. The series ends with House and Wilson riding into the sunset together to the tune of "Enjoy Yourself", the song that Wilson's girlfriend Amber performed at the end of Season 5. The last scene wouldn't have been out of place in a romantic comedy.
In one scene House checks Wilson's temperature by touching his forehead with his.
Wilson gives House an expensive book for Christmas, with a note "Greg - Made me think of you". The team is ready to belive it's from House's love interest, because of the pretty romantic message on the note and Wilson's "girly" handwriting.
House: What makes a guy start drooling? (pause) Chase, were you wearing your short shorts?
The "I'm gay" quote from "The Mistake" that most people cite as House/Wilson Ho Yay actually leans more toward House/Chase, since he was explaining that he didn't fire Chase because he has great hair.
In the same episode, House insists that Chase loves him. Wilson replies that Cameron loves him, Chase merely loves his job. Despite House's "The Reason You Suck" Speech to Chase earlier in the episode, House looks genuinely hurt by the idea that his little wombat doesn't love him.
It seems everyonefinds Chase ungodly attractive — In "Ugly", House ponders aloud whether Foreman might be gay because he was unaffected by a pretty woman whom House couldn't think logically around. Wilson, without missing a beat, asks "Did he turn into an idiot around Chase?"
In "House Divided", just after Cameron and Chase get engaged, House addresses her as "the soon-to-be-second-prettiest Dr. Chase".
In "Half-Wit" from season 3, Chase thinks House has terminal brain cancer and attempts to comfort him:
House: Well, if you're considering grabbing my ass, don't start anything you can't finish.
From the same episode, after Cameron tries to kiss House as a pretext for drawing his blood, since she also thinks House has terminal brain cancer.
House: Foreman and Chase's lips aren't getting so close, now that I know your plan.
In the Vogler story arc from season one, House is instructed to ax one of his team for budget reasons. Here.
House: [Keeping all 3] will be more cost-efficient, once I've grabbed Cameron's ass, called Foreman a spade, and Chase... well, I'll grab his ass too.
In "Parents":
House: Chase is right. All parents screw up all children. He's also dreamy, but that's not relevant now.
In season 2, the House/Chase Ho Yay spilled over into the blooper reel included on the DVD release. During a scene in which Chase angrily confronts House, one of Hugh Laurie's flubs has him saying, "[Chase's] hair is adorable; I don't deny that - the figure is svelte!"
And in an episode from the fourth season, we get another "I love you", said by Kutner to House when House tells the group to say what they think he wants them to say... add this to Kutner being utterly thrilled when he discovers he's House's Secret Santa, and you start to wonder why nobody else seems to be noticing these things.
Kutner took Cole out to a magic show in "You Don't Want to Know". House even calls Cole out: "You have to leave work at 6 p.m., but you make time for man dates?" In the same episode, we also find out that Kutner has babysat Dr. Cole's son.
There's Tritter and House, as well. Ever since their first meeting in "Fools For Love", where House anally inserted a thermometer into Tritter and just walked away and left him there (because Tritter tripped his cane out from under him, making him slam into the door), Tritter becomes completely obsessed with House. He pretty much spends all his time stalking House, questioning all of House's friends trying to find things on him, and searching his house. He also actively sought out arresting House, and did a body search on him, which consisted of him groping House and lifting up his shirt (which exposed House's abdomen).
From "Recession" we have the Ho Yay banter between Foreman and Taub, including being compared to Bert and Ernie (Taub's Ernie).
Foreman: Are you wearing my tie?
Taub: I saw it in your closet, and it happened to match my shirt.
Foreman: Why were you in my closet?
Taub: Looking for a tie. What's the big deal?
House: Obviously, he wants you out of the closet for some reason. I suspect marriage, but I'm liberal that way. source
Season 8 starts on with some blatant House/Foreman subtext. Foreman is now in position of power, which makes the dynamic between him and House somewhat similar to that between House and Cuddy. Also, there's that time in "Risky Business" when House grabbed his ass...
In "The Down Low", House gushes over the fact that the patient of the week is a drug dealer, leaving the team with almost no medical history
Thirteen: So he's dangerous and withholding, which you find irresistible, but guys like that, they never call
In season 7, "The Choice," Wilson tries to get the team to occupy House so he can have some privacy. "Taub asking me out was quirky, but Thirteen? That's a barking cat... Why set me up with a hottie I can't sleep with? And Thirteen."
With Foreman in Season 8, episode 4, "Risky Business". House grabs Foreman's behind. "What are you doing?" "Holding your ass." (Expecting Foreman to hit him). "My God, you have superhuman discipline. And GLUTES!"
In season 6, "Baggage", there's serious subtext between House and Juan "Alvie" Alvarez, who's living under his roof for the episode. Dr. Nolan runs parallels between House's relationship with Alvie and House's relationship with Wilson, and at the end of the episode House gets drunk because Alvie left his place to go to his cousin's place in Phoenix.
While House was in prison, nazi guy Mendelson gets pretty leery with him, squeezes him for vicodin, shoves him to the floor and takes his cane. House for his end looks genuinely afraid around him most of the time, and in the next episode tells people/Wilson that he was raped on some level in a stridently awkward Let Us Never Speak of This Again kinda way.
out of "some secret and very unconscious desire to get Wilson into my bedroom". There is no clue in his sleep-deprived tone to how sincere or not he's being.