The above graphic was just for kicks. If you hover over the individual episode thumbnails, you can click on "Watch This Full Episode" and in three cases (Goobacks, Chef Goes Nanners, and Super Best Friends), the "Watch This Full Episode" link takes you to the wrong episode. That's carelessness on the part of the South Park website. Luckily, all the episode links below are correct.
So here are my top episodes, but I will have you know that I have not watched every single South Park episode ever so these favorites could change. (I've watched a heck of a lot of episodes though!) Also, I didn't watch these episodes back-to-back so the order's pretty arbitrary. (Even if I had watched them back-to-back the order would still be pretty arbitrary; I'm no master at picking favorites. Actually though, the first three, the Imaginationland trilogy—there's almost no doubt that those rise above the others.)
Here's the links; each episode has its own Wikipedia article, hence the clickable Wikipedia icons; all the descriptions are taken from the South Park website. Oh, and let me say that bit about Wikipedia again: each episode of South Park has its very own Wikipedia article. And they're not stubs either. I love Wikipedia.
And just a note: I probably shouldn't have to tell you that you shouldn't expect to get all the jokes in an episode of any TV show but I'm telling you it just in case. This is true for the usual reasons and sometimes episodes of South Park contain references to past episodes. Pretty much all the episodes of South Park that I have ever watched—I've watched by going to the South Park website and clicking the "random episode" button; and I'm sure I've missed some references to previous episodes but it doesn't really matter. Hopefully. In most cases.
Imaginationland Episode I
"When the entire contents of the world's imagination lay open before them, Stan and Kyle step right in. Back in South Park, Cartman swears he's seen a leprechaun."
Imaginationland Episode II
"After the wall in Imaginationland is blown up by terrorists, the evil side crosses over. Cartman tracks down Kyle and Stan at the Pentagon and demands Kyle makes good on their agreement. Meanwhile, U.S. troops cross over into Imaginationland while evil characters cross over into reality."
Imaginationland Episode III
"Inside Imaginationland, Stan and Butters engage in the battle of their lives as they fight the army of evil imaginary forces. Meanwhile, Cartman goes all the way to the Supreme Court to get Kyle to pay up on their bet."
The Death of Eric Cartman
"Butters is freaked out when he thinks he can communicate with the dead. Although his parents have made it clear to him there is no such things as ghosts, Butters is sure one is haunting him. Butters knows he has to give up his ghost pal or be put into a mental institution."
Butters' Very Own Episode
"Butters inadvertently reveals a deep, dark family secret about his father's late night "shopping" sprees. Alone and lost, Butters determinedly makes his way through porn theatres and gay bath houses in an effort to get his dad back home in time to eat at Bennigan's for his parents' anniversary."
You Have 0 Friends
"Kyle 'friends' the wrong person on Facebook, and all of his friends abandon him as a result. When he becomes desperate for just one person to friend him, he turns to Stan. But when Stan tries to help, his Facebook account goes rogue, and he finds himself in the digital realm forced to battle his own profile."
"Humans from the year 3045 are traveling to South Park through a recently discovered time portal and are looking for work. When the boys try to earn some extra money, the time-traveling immigrants are willing to do the same work for next to nothing, causing the boys to lose their jobs."
Chef Goes Nanners
"Chef's passionate protest declaring the South Park flag racist enflames the entire town. The kids separate into two opposing camps and prepare to debate the issue. Stan and Kyle champion the current flag while Wendy and Cartman head up the side for a new flag. Wendy finds herself strangely attracted to Cartman."
The Losing Edge
"A winning season and overzealous parents threaten to ruin the entire summer when the boys of South Park head to the Little League State Championships. The kids desperately want an end to the boring baseball season, and just one loss would set them free. Unfortunately, the opposing team is much better at losing than they are."
Best Friends Forever
"Kenny is the only one of his friends to get the newest, coolest portable gaming device and Cartman can't deal with it. Will they remain best friends forever?"
Super Best Friends
"Stan, Kyle, Cartman and Kenny discover David Blaine, magician and cult leader, performing in the streets of South Park. Stan finds out early that the Blainiacs are not as nice as everyone thinks. He tries to convince the other boys they've been brainwashed, but they have forsaken their friends and families. Teaming up with Jesus, Stan calls upon all the Super Best Friends to destroy the magician and thwart the mass suicide pact he has launched."
Hell on Earth 2006
"Satan is throwing the biggest Halloween costume party ever and no one will be admitted without a wristband. Satan is busy checking the R.S.V.P. list and deciding what costume to wear to the big event. Every detail must be perfect for the prince of darkness. But even Satan can't foresee everything."
"Randy steps forward with a solution to fix the desperate financial state everyone finds themselves in. The town gets behind him and everyone starts to live a life that no longer depends on any economy at all. Meanwhile an unlikely savior makes the ultimate sacrifice to solve everyones problems."
Dances With Smurfs
"Eric Cartman seizes the opportunity to become the voice of change at the school when he takes over the morning announcements. His target is South Park Elementary's Student Body President, Wendy Testaburger. Cartman is asking the tough questions and gaining followers."
I'm a Little Bit Country
"The boys join some anti-war protesters because it's a free pass out of school for the day. Their simple plan to protest their way out of class goes south when they find themselves in the middle of the two opposing sides of the issue. Meanwhile, Cartman attempts a flashback to 1776 to avoid studying for his American History assignment."
UPDATE (April 21, 2011):
A small but important update has been made to this list.