South Park has many jokes concerning Stan and Kyle's deep friendship.
Early on, in Two Naked Guys in a Hot Tub, Stan's father tells Stan he should hang out with Kyle less because people will think they're "funny".
In Cheroke Hair Tampons Stan was willing to give up his kidney to save Kyle. He also said he "didn't want Kyle to die until he did."
The Imaginationland trilogy included Kyle communicating with Stan psychically when they're in different worlds. Super best friends indeed.
The episode "Guitar Queer-o" plays like a break-up/make-up love story between Stan and Kyle, complete with Stan declaring "I need you." to Kyle at the emotional climax.
At the end of "Super Best Friends", Stan and Kyle announce their super best friendship, to which Cartman responds
"The China Probrem" features the most blatant Ho Yay ever: Stan and Kyle, sobbing in each others arms after Indiana Jones' Canon Defilement, outright saying "I love you!" to each other while caught in the moment. Shipping backlash in 3, 2...
The egg episode with Stan and Kyle basically functions like the episode "Guitar Queer-O" in some parts. "Nice hat," indeed.
The episode name is "Follow That Egg"; in it, Stan and Kyle are the reason gay marriage gets legalized in Colorado. It's complete with lines like:
Mrs. Garrison: How 'bout our gay couple: Stan and Kyle?
Smug Alert!: Stan is crushed when he realizes that Gerald is forcing Kyle to move to San Francisco, and declares that he'll find a way to get everyone to drive Hybrid cars just to have his friend back. The rest of the episode is him trying to contact Kyle and fretting over his safety. Not to mention the hug Stan gives Kyle when he returns to South Park that definetly gets an "AW" from the fangirls.
The episode "Ass Burgers" is chock full of it. Stan and Kyle act like they're just broken up. Stan even says 'I love you,' to Kyle. Twice.
That entire scene plays out similar to an enstranged (and violently drunk) ex trying to rekindle with an old flame whose moved on. Perhaps it's just me, but it sounded very Love Triangle - esc, what with Kyle talking about he's with Cartman (Burger) now, so he and Stan can't just go back to being friends.
In The Return of Chef, Stan and Kyle hug and watch the sun set together.
The two can be seen hugging or sleeping on each others' shoulders many times throughout the series.
In Death Camp of Tolerance, while Mr. Garrison is spanking Mr. Slave, the whole class looks on in horror... with the exception of Stan, who is staring at Kyle.
Cartman/Kyle
Cartman can be a little too obsessed with Kyle.
In the movie when Cartman and Kyle think they're about to die Cartman apologizes to Kyle for all the crap he's given him over the years.
There was also a three-part episode with a subplot consisting of Cartman trying to force Kyle into oral sex.
In the commentary for that episode Matt and Trey make it clear that Cartman trying to get Kyle to lick his balls isn't sexually motivated and he just wants to humiliate Kyle
At the end of Part I of that trilogy, Cartman takes out a photo of a sweet, innocent-looking Kyle and lustfully traces his finger across Kyle's lips, while saying, "Make no mistake, Kyle. Before this is over, you WILL suck my balls."
One has to question whether "lust" was ever at play here...
In Fun With Veal Kyle comes very close to kissing Cartman's ass to save some baby cows.
In Man Bear Pig Cartman hovers over Kyle while he is sleeping.
Later, Kyle risks his life to save Cartman from drowning.
In the episode "It's a Jersey Thing", we get this.
Cartman: You saved my life, Kyle. Deep down inside you're a monster. But you're my little monster.
Throughout Smug Alert, Cartman expresses nothing but joy that Kyle and his family no longer live in South Park, and he uses Butters as his "Jew Substitute", but quickly comes to realize that without Kyle to rip on, his life is empty and shallow. In order to correct this, Cartman braves his way through the San Francisco smug storm and risks his own life just to save Kyle and his family. In the end, when the Broflovskis make it back to South Park, Cartman keeps quiet about what he'd done, sheding his usual Jerkass behavior to achieve a very rare moment of Humble Hero.
Tonsil Trouble. Cartman gives Kyle AIDs and the two must travel together crosscountry to find a cure. Kyle will angrily and frequently remind or tell people that it was Cartman's fault that he has HIV, and is met with many, many gay jokes. Not to mention the massive amounts of Foe Yay.
Kyle: "Oh please, no reason! I got AIDS from him!"
Airline Worker: "Oh, so you boys are like that, huh?"
Kyle: "NO!"
Announcer: "These brave friends-"
Kyle: "Oh stop! We're not friends! He's the one who infected me with AIDS!"
Announcer: "...These brave lovers..."
When Kyle and Cartman were on the plane to visit Magic Johnson, it looked like Cartman tried to hold Kyle's hand.
Actually, Cartman did try to hold Kyle's hand on the plane, but let go after Kyle's angry "Don't. Touch. Me."
The ending of "Le Petit Tourette": After Kyle thwarts Cartman's plan to be shown on TV with "tourette's," Cartman hugs Kyle and says, "You do care!" (since he had lost the ability to filter his thoughts and would have ended up blurting out embarrassing secrets to a national audience). Meanwhile, Craig informs Thomas that he is the coolest kid he's ever met and asks if he could do his laundry sometime. One of the embarrassing secrets Cartman would have admitted, by the way, was an experimental homosexual act he committed with his cousin.
Cartman: My cousin and I touched weeeEEEE...WEEN-ter is a very cold time of year!
It seemed to me like Cartman was trying to kiss him.
Oh and this little gem:
Butters: Wow, you really know what you're doing.
Cartman: Yeah, I sneak into Kyle's room lots of times.
In "Kenny Dies", Kyle sees Cartman crying and hugs him while the two cry together. At the end of the episode, when it turns out it was just a scheme, Kyle says "I don't believe it... I actually held you in my arms and cried with you!"
In "Funnybot" the translation for part of what Cartman tells the Germans about Kyle is that he's:
Cartman: A handsome soft Jew. He's fresh. And beautiful, beautiful.
In recent episode Crack Baby Athletic Association, Cartman and Kyle sit together naked in a hot tub full of KFC gravy. While eating french fries. The French call it "boutine".
In the same episode, Kyle attempts to explain to Cartman his plan to build a crack-baby orphanage out of their profits. Cartman is so happy with the idea (because it will get the public on their side) that he pulls Kyle into a hug. Kyle finds it slightly worrying.
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Hell, Cartman performed oral sex on Butters while he was passed out and took pictures of it, and even had the balls (*ahem*) to say that Butters was the gay one.
Not to mention the throwaway lines about Cartman which includes him acquiring semen by orally pleasuring a man. Or his obsession with Mel Gibson. Or that time he whacked off Ben Affleck...or Stan's dog...or Leonardo DiCaprio.
From "The Death of Eric Cartman":
Cartman: Clyde, can you feel me? Feel me, Clyde!''.
What tops this all off is the time where Butters spends the entirety of "Super Fun Time" escorting Cartman by hand. This invokes a very predictable response.
According to Word Of God, Kyle is the "most likely" to grow up to be bisexual.
Hmmm? Source or it didn't happen.
Not sure where that theory came from, but in this interview, Trey Parker says the one most likely to grow up to be gay is Stan. Guess that whole Wendy thing might not be as perfect as it seems.
That's funny, especially since this was much earlier in the series and Stan was still basically just Trey Parker's avatar.
Not to mention Cartman walking in on Butters in the bath.
And how he holds Butters' hand... While he's still in the bath.
In "Goobacks", the episode with the immigrants from the future, all the men in South Park are trying to stop the future from happening in order to solve the immigration problem. Their solution? Gay orgy.
Not just the men. Stan, Kyle, Cartman, and Kenny walk off-screen with them at the end of the episode... hinting that they join the pile.
Actually, I'm pretty sure they were leading the pile.
Craig vs. Tweek is full of Ho Yay quotes; Craig and Tweek are also very Ho Yay.
Near the beginning of Tonsil Trouble, Butters kisses Eric in front of a room of people.
Stan's dad and Kyle's dad also masturbated together in a hot tub.
Does this count?
Terrance: That Scott really hates us.
Phillip: Yes, perhaps he's homophobic.
(Silence)
Terrance: But we're not gay, Phillip.
Phillip: We're not?
Matt and Trey themselves have a few moments during the DVD foreward for Cartman Gets An Anal Probe.
In "Fat Camp" Kenny gave Howard Stern oral sex.
In "Make Love, Not Warcraft" during the meeting to form a plan against the player who keeps killing them, we get this dialogue.
Cartman: When Hitler rose to power, there were a lot of people who just stopped playing. You know who those people were? The French. Are you French, Clyde?
Cartman is the first person to notice Butters has gone missing in 'Last of the Meheecans'. In the context of the episode, it's not much - Cartman just wants to win the game - but given that Cartman and Butters have a fairly deep friendship in other episodes...
Damien and Pip have a bit of this in season one.
Bradley and Butters in Cartman Sucks.
Kyle and Kenny is arguably the second most popular pairing in the fandom (after Style, sometimes behind Kyman). This may be because of their game of spitting in each others' mouths, or because kyle seems to be the only one to show concern for Kenny throughout the show.
Mysterion, later revealed to be Kenny, seeks out Kyle for help by sneaking into Kyle's room through his window.
Stan and Kenny have their share, too. In Kenny Dies, Stan is the most upset about Kenny's illness, and later Kyle tells Stan that Kenny's last words were "Where's Stan?"
