I haven't been a very consistent "South Park" viewer. I started watching regularly from around the fifth season in 2001 until the 13th season in 2009. That's roughly the same amount of time covered by the early episodes of "The Simpsons" I wrote up a previous list for, so while this one isn't all-inclusive, I feel sufficiently well-informed. And as I don't think I'm a typical "South Park" viewer, some of these choices are probably going to strike more ardent fans as a little odd.
As usual, episodes are ordered by airdate, and I will cheat and count multiparters as single entries. Spoilers ahead.
"The Spirit of Christmas" - The first episode of "South Park" to air may have been the one with Cartman and the anal-probing aliens, but the true genesis of "South Park" was a pair of crudely made short films depicting beloved Christmas icons fighting for domination over the holiday season. Jesus and Frosty the Snowman brawled in the first short, a student film, and Jesus went on to fight Santa in the follow-up, commissioned by a FOX executive as a video Christmas card. The shorts were viral videos in the pre-internet age, and are still very funny and impressive today.
"Scott Tenorman Must Die" - The episode where Cartman went too far. "South Park" was always known for pushing people's buttons with its unapologetic crudeness and adult humor. Kenny dying every week was already considered plenty subversive. However, the sordid tale of Cartman seeking revenge against Scott Tenorman is where the show really started testing the limits and seeing how far it could go. What sells it for me is how self-aware the creators are about what they're doing, with the Radiohead cameo and the Looney Toons bullseye as the perfect finishing touches.
"The Return of the Fellowship of the Ring to the Two Towers" - As much as I respect their way with social commentary and more ambitious "Imaginationland" style high concept epics, many of the best episodes of "South Park" are the ones that are actually the truest to life. The boys accidentally getting ahold of a porn VHS was taken directly from the childhood experiences of one of the directors, though the various wild hijinks that ensue (and digs at "Lord of the Rings") reflect the present times. And I love Butters turning into Gollum and obsessing over his "precious." He's probably my favorite character.
"Ginger Kids" - I don't find Cartman entertaining, but he's such an important part of why "South Park" works. Here, he starts a wave of oppression against redheaded kids, and when the other boys try to give him a taste of his own medicine, essentially creates a Nazi cult in retaliation. I love the ridiculous and very specific complaints against the "gingers," the way that the commonly used "Black Like Me" teaching tactic backfires completely, and how of course Cartman doesn't learn a thing from the whole escapade. And what really gets me is that "Ginger Kids" was actually inspired by a real anti-ginger bullying incident.
"Trapped in the Closet" - I'm not going to say that "South Park" was responsible for turning Scientology into the laughingstock it is to most of us today, but boy did it help. The creators didn't hold back, strongly implying A-list movie stars Tom Cruise and John Travolta are gay, excoriating Scientology texts as nonsense ("This is what Scientologists actually believe"), and flat out accusing the "church" of being a scam. The controversy only put the show in a better light, and gave Trey Parker and Matt Stone more of a spotlight. This is the point where "South Park" started being recognized for its satirical fearlessness.
"The Return of Chef" - Alas, the "Closetgate" controversy spurred the end of one major relationship. Isaac Hayes, the voice of Chef, left the show over "Trapped in the Closet." Hayes hadn't made regular appearances for some time, but it was still a bit of a shock. Parker and Stone gave him a fitting sendoff, pasting together a final performance from previously recorded dialogue, depicting his character as brainwashed by child-molesters, and then graphically killing him off. It was simultaneously very touching, totally disgusting, and petty as hell. And I'm so glad that "South Park" had the guts to do it.
"Fantastic Easter Special" - The "South Park" kids try to figure out what bunnies and Easter eggs have to do with Jesus's resurrection, revealing a secret society that reveres rabbit popes, who were wrongly ousted by the Catholic Church long ago. The story pokes a lot of fun at Christianity and various religious figures, but not in a particularly provocative or confrontational way. I just find it endlessly charming and creative, from the Latin version of the "Peter Cottontail" song to the delightful return of ass-kicking Jesus. There aren't many Easter cartoons out there, but this is by far my favorite.
"Britney's New Look" - This is my favorite episode of "South Park" because of how utterly sick, and yet how perceptive and humane it is. Britney Spears comes to South Park fleeing the paparazzi, and is driven to attempt suicide. She fails, and goes through the rest of the episode with most of her head missing, which nobody seems to notice. The ending involving ritual sacrifice, Miley Cyrus, and the boys essentially giving in to peer pressure, is very disturbing and uncomfortably on point. During Spears' meltdown debacle, she got a lot of sympathy, but not many were willing to call out who was actually responsible - the audience.
"The China Problem" - As the child of very pro-China immigrant Chinese parents who wouldn't be caught dead in a P.F. Chang's, this episode was meant for me. I found Cartman's paranoia towards yellow invasion absolutely hysterical. However, the episode is better known as the one where Steven Spielberg and George Lucas violate Indiana Jones physically, having already done the job metaphorically in "Indiana Jones and the Kingdom of the Crystal Skull." The pair had been ragged on before in "Free Hat" for going back and "fixing" their older films, but this time Parker and Stone went full "Deliverance" and really let them have it.
"201" - Finally, we close out with the most notorious episode of "South Park" to date, and I still haven't seen it in the way that the creators intended me to. This is because Comedy Central caved under pressure, and not only censored the image of Muhammad from the entire episode, but bleeped all mention of him as well. I fully admit that "201" is on this list purely because of what it represents in the American media landscape, rather than for its actual content. Parker and Stone figured out exactly how far artistic speech could go in this country, and got everyone to pay attention.