This pair is controversial for the April Fool's episode that came between them: "Not Without My Anus." Fans were pissed off that Seaeson 2 didn't begin with a resolution, and they flooded Comedy Central with complaints about it.
S10 E03 "Cartoon Wars"
S10 E04 "Cartoon Wars, Part 2"
S14 E05 "200"These two pairs have one thing in common: Muhammad. He was not shown in any one of these four episodes, but it is the second pair that remains banned.
Matt and Trey did show Muhammad in the "Family Guy" segment in "Cartoon Wars Part II," but Comedy Central blacked it out before air. Matt and Trey then inserted a message where the clip was explaining the situation. South Park Studios were asked about the existence of Muhammad in the clip, and Anne Garefino assured us that it does exist, hoping that we'd get to see it someday. Ten years later and counting, that day has not arrived.
Matt and Trey hinted at showing Muhammad in "200" and "201," but in the end they didn't. Comedy Central, having no Muhammad to black out like it did in "Cartoon Wars Part II," instead bleeped some speeches at the end of "201." Comedy Central then prohibited repeats of the episodes because of the violent reactions to them from some Muslims and warnings about what could happen to Matt and Trey for depicting Muhammad.
S15 E07 "You're Getting Old"
S14 E06 "201"
S15 E08 "Ass Burgers"
This is the pair in which Trey contemplated making lasting changes to the show, but ultimately decided these changes weren't going to work. The changes to the Marsh family and Stan's darkening mood in "You're Getting Old" had people saying that the show was going to end right then and there, in the summer of 2011. Trey was very surprised that people thought the show was ending. "Ass Burgers" has the Marsh family getting back together and moving back home and Stan feeling better about the future.
No controversy here
S04 E09 "Do The Handicapped Go to Hell?"
S04 E10 "Probably"
The Catholic episodes, wondering what happens to handicapped people who may not have a sense of right and wrong due to their disabilities, when they die.
S10 E12 "Go God Go"
S10 E13 "Go God Go XII"
The atheistic episodes, where religion is gone and been replaced by various denominations of atheism. Science has replaced God as something to be worshiped.
S12 E10 "Pandemic"
S12 E11 "Pandemic 2: The Startling"
This pair is just spoofing monster, disaster and epidemic movies, with giant guinea pigs being the monsters.
S18 E09 "#REHASH"
S18 E10 "#HappyHolograms"
The social media episodes, where Twitter and Let's Plays have changed the way we communnicate and play online, and how that's affected our real lives. They are the culmination of other episodes that addressed Oculus Rift and other forms of media that didn't exist a decade ago, as well as such things as drones and share ride services.
The Three Parters
S03 E07 "Cat Orgy"
S03 E08 "Two Guys Naked in a Hot Tub"
S03 E09 "Jewbilee"
This set is the Meteor Shower Trilogy, because they all take place on the same night, in three different settings. "Cat Orgy" focuses on Cartman and Shelley when Liane goes to the meteor shower party at Mr. Mackey's house and hires Shelley as a babysitter. Skyler appears as the boyfriend Cartman has to get rid of for Shelley's sake. "Two Guys Naked in a Hot Tub" focuses on Stan and Butters, as well as on Dougie, at the party. This is Butters' breeakout episode. "Jewbilee" focuses on Kyle and Kenny and features Moses, who is one of the Super Best Friends two years later. Ike also appears as a Squirt.
S11 E10 Imaginationland: Episode I
S11 E11 Imaginationland: Episode II
S11 E12 Imaginationland: Episode III
This set was made in the summer of 2007 and was meant to be a movie, but Trey broke it up into three episodes so he could fill out Season 11. Butters was the Chosen One here. The trilogy was reassembled and released as a DVD later on.
S17 E07 Black Friday
S17 E08 A Song of Ass and Fire
S17 E09 Titties and Dragons
This set is modeled on the Game of Thrones series and the books they're based on. Here is where Kenny becomes a real Japanese princess.
S07 E14 Raisns
S12 E14 The Ungroundable
S17 E04 Goth Kids 3: Dawn Of The Posers
This set can be called the Goth Kids Trilogy. Each episode introduced us to another clique. "Raisins" introduced us to the Raisins girls, who work in a Hooters-style restaurant and named themselves after high-end cars. Butters fell in love with one of them. "The Ungroundable" introduced us to the Vamps. Butters becomes ungroundable. "Goth Kids 3: Dawn Of The Posers" introduced us to the Emos, Edgar Allen Poe, and again to the Vamps. As you can see, there are five seasons between eps. If there is a Season 22, we could see a fourth Goth Kids episode. :)
The Four (Or Five) Parter
S13 E02 The Coon
S14 E10 Coon 2: Hindsight
S14 E11 Mysterion Rises
S14 E12 Coon vs. Coon & Friends
S15 E14 The Poor Kid (honorary mention)
This set is the Coon series, by the end of which the Coon has lost all support from his friends and has made a very powerful friend in Cthulhu. Mysterion figure in all of these episodes, but if we change the focus from The Coon to Mysterion, then a fifth episode can fit in. "The Poor Kid" has Mysterion protecting his sister when she calls out to him.
S19 E07 Naughty Ninjas
S19 E08 Sponsored Content
S19 E09 Truth And Advertising
S19 E10 PC Principal: Final Justice
The entire 19th season revolved around PC Principal and the fourth grader Leslie Meyers, but these four form the climax to this story arc. The climax begins with the newsmen asking Officer Barbrady about Leslie at the end of "Naughty Ninjas" and continues through her death at the hands of PC Principal after he learns that she's an ad, one of many that are subverting life in South Park.