"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.
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.
Kyle has a picture of him and Stan smiling while holding each other that he must often keep with him.
We see this in "Asspen": after Stan tells Kyle he's going to ski down a dangerous slope, Kyle is later seen staring at the picture with a worried expression on his face.
Stan and Kyle pose for a picture by holding hands when they get the definition of the word "fag" changed from an insult toward homosexuals to instead mean annoying Harley riders.
Also earlier in that episode, when the adults think the kids meant "fag" as a slur against gay people, Mr. Mackey expresses his shock that Stan and Kyle in particular would show any intolerance toward gay people.
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.
Imaginationland's subplot consists of Cartman trying to force Kyle into oral sex.
Averted, 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."
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.
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.
"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.
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.
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.
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.
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.
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.
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.
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...
More or less, the entirety of both Awesome-o and Super Phun Time (the latter essentially an episode where Cartman and Butters go on a date).
In Casa Bonita: "Eric, you're the best friend in the whole world. I-I love you..."
Butters and Cartman wrestling at the beginning of "WTF".
In "Li'l Crime Stoppers", Butters finally extracts a semen sample. How did he do it? He thought about Stan's mom's boobs. But remember what happens in "Pre-School"? The kids couldn't/weren't willing to get an actual picture of Stan's mom's boobs, so they took a picture of Cartman's ass with nipples drawn on it instead. So if Butters has never seen her naked boobs for real, what was he picturing?
In season 4, episode 2 we have this gem: "All that time, we didn't understand what a unique and magical ass it was." note To put this into context, Cartman is in juvenile detention because he threw a rock atToken, and the boys are at risk of losing a sled race to the girls, and the force of Cartman's weight gives their sled more speed. But taken out of context, Butters just sounds really enthusiastic about Cartman's ass.
Cartman hugs Butters after Butters gets his first kiss.
Oh, and in the movie, before Butters even had a name, we get this absolute gem:
Cartman: Yes, I saw the Terrance and Philip movie. Who wants to touch me? [Beat] I said, who wants to fuckin' touch me?
Butters: *pokes at Cartman, clearly interested* Ooooooh...
Butters gives Cartman a hickey in "The Ungroundable".
Butters comforts Cartman after Token and Nichole's breakup in "Cartman Finds Love".
In "Going Native", Cartman is extremely jealous of Kenny when Butters claims that Kenny is his best friend.
Kenny and Butters have had a number of moments themselves throughout the seasons are shown to be very close.
Butters shows affection for Kenny in "Major Boobage" by holding him and is the only one to show sympathy for him when Kenny is high.
Butters states that Kenny is, as of "Going Native", the only person at school Butters likes.
This causes Cartman to respond with "You guys gonna make out, Kenny?"
That episode in general is full of Ho Yay moments between them, including multiple scenes where they're holding hands.
Butters drew a picture for Kenny of him and Kenny together in an airplane in "Kenny Dies".
Kenny is both physically and emotionally sweet and comforting to Butters in "Lil' Crime Stoppers" while playing "Good Cop".
Kenny and Butters hug each other while everyone else just high fives when Stan and Kyle reach 100,000 points in "Guitar Queer-O".
Butters was really upset when he found out Kenny had a girlfriend in "The Ring" and even called Kenny's then-girlfriend a "total slut."
In the video game South Park: The Stick of Truth (which is considered canon to the show), Butters even admitted to having a crush on Princess Kenny. Even though Kenny was roleplaying as a chick, it wasn't as if Butters didn't know it was just Kenny wearing a dress.
One of the embarrassing secrets Cartman would have admitted, in "Le Petit Tourette", 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!
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!''.
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?