"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.
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?
In "The Jeffersons", when Stan hears a knock outside of his bedroom, he immediately assumes it's Kyle. And in "Crack Baby Athletic Association", he is completely unfazed at finding Kyle is his bedroom past midnight, leading to the assumption that this is fairly common.
In "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.
"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 who's moved on. Perhaps it's just me, but it sounded very Love Triangle- esque, 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 beginning of "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.
According to (conflicting) Word of God, Kyle and/or Stan were considered "most likely" to grow up to be bisexual/gay.
Cartman can be a little too obsessed with Kyle. A lot of his antics involve humiliating Kyle sexually in some way. And while it sure ain't a healthy relationship, it does get very intimate sometimes.
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.
Imaginationland's subplot consists of Cartman trying to force Kyle into oral sex.
Admittedly 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 the 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 "ManBearPig" Cartman hovers over Kyle while he is sleeping.
Later, Kyle risks his life to save Cartman from drowning.
In "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, shedding 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?"
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."
Cartman: Yeah, I sneak into Kyle's room lots of times.
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). Keep in mind that he couldn't lie at that point. 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!
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.
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.
In Faith Hilling, after Stan and Kenny abandon the meme all four of them had sworn to stick to for TaylorSwifting, Cartman holds an enraged Kyle and the two walk away together. They later sit together and share a quiet moment, in which no fat or Jew jokes pass between them.
Jewpacabra is yet another episode focusing on Cartman's usual antisemitic antics, with Kyle taking on the role of the exasperated straight man once again. What's different about this episode, however, is that despite having the perfect opportunity to watch Cartman get his just deserts, Kyle decides to save him. And get him a blanket. And tuck him into bed.
I Should Have Never Gone Ziplining has Cartman and Kyle sitting next to one another on the shuffle (closely, since the shuffle is rather full), and, once Stan admits that he betrayed the other three so he could get a free iPod, Cartman comforts Kyle while the latter has a minor breakdown.
Cartman Finds Love takes this to its most extreme. Cartman tells the whole school that he and Kyle are a gay couple and even tells Nicole "stay away from my man, bitch!" Later he confesses his love for Kyle in front of an entire basketball game, claims that "there's magic when they kiss" and serenades him while a heart forms around them on a giant screen. Hard to get any less subtle than that.
Note that the episode's synopsis says "Now, to make sure nobody gets in the way of true love, it is time for Cartman to finally let someone know exactly how he feels." The "true love" was initially meant to trip the audience up, and make them believe he was in love with Nicolenote especially the pre-air ad for the episode (when he really wants her to end up with Token). So, that special "someone"? Kyle, aparently.
The episode almost seems like a shot directed at shippers and shipping in general.
Obama Wins! continues the trend with Cartman (regarding Kyle) saying "Run now, Little Firefly", reminiscent of Hannibal Lector talking to Clarice Starling (whom Hannibal became obsessed with and stalked, watching her sleep and touching her hair). Also, near the end of the episode, Cartman saved Kyle's life, preventing him from getting shot by General Tsao.
In Cartman Sucks, Cartman took a few, ahem, compromising photographs of himself performing oral sex on Butters. When Kyle finds out about this, Cartman threatens to photoshop Kyle's face over his own. Later, when the photos go missing, Cartman immediately assumes that Kyle has them.
Cartman once performed oral sex on Butters (hence the Pun-Based Title "Cartman Sucks") while he was passed out from cold medicine 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.
And then there's the time he walked in on an "indecent" Butters in the bath during "The China Problem". Even holding his hand... while he was still inside the tub.
Near the beginning of Tonsil Trouble, Butters kisses Eric in front of a room of people to show him that he's not afraid to touch him.
"Super Fun Time" involves Butters spending an entire field trip escorting Cartman by hand. This invokes a very predictable response.
Of all the townspeople, Cartman is the first—and most eager—to try Butters' "creamy goo" in "Sarcastaball". As in, the "goo" that builds up inside of Butters and comes out at night when he thinks about girls.note Or perhaps another certain 4th grade student...
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...
From "The Death of Eric Cartman":
Cartman: Clyde, can you feel me? Feel me, Clyde!''.
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?