In Dressed To Kill, Eddie Izzard called out his audience for not knowing who Lafayette was.
In his HBO special Complaints And Grievances, George Carlin mentioned pussy farts as something people don't talk about in public. He opened his next HBO special by saying the very same thing, adding "apparently some people don't know what a pussy fart is, because I got some inquiries." He then explained the concept.
In the Total Drama story, Legacy, Trent identifies Utopia Limited — one of the least known of the Gilbert and Sullivan operettas — only as "some old musical" because he didn't remember the name and couldn't be bothered to look it up. The narrative expressly notes that the song from Utopia, Limited that became the basis for Trent's tribute song is quite obscure.
Marik Plays: Slender: The Arrival includes a reference to Richard Linklater's "Before Sunset". Marik immediately points out it's the most cultured and obscure joke he's ever made. "Drink that in, 'cause it's never going to happen again. From now on, it's just poop and fart jokes."
hbi2k calls some of his jokes "2 percenters" based on how much he thinks his viewers get them.
In Dragon Ball Z Abridged, after they'd been talking about Raditz, Nappa asks, "But what about the Fraggles?" Vegeta answers "No one is going to get that reference, Nappa."
Kiss Kiss Bang Bang. When two goons appear to accost Harry, one of them introduces himself and his colleague as "Ike, Mike, and Mustard"note Salt, Pepper, and Mustard, your standard-issue dinner condiments. Harry doesn't get it, and even the other goon outright agrees that it's pretty damn obscure, and the two start arguing over it.
Inverted in The Avengers. Almost all of the modern well-known cultural references are lost on Captain America, who has been frozen since World War II. When someone makes a reference to The Wizard of Oz, he's delighted to be able to point out that he actually got it. In The Winter Soldier it's revealed he has a list of pop cultural things he has to experience, like Star Wars and thai food.
In the Arrested Development episode "S.O.B.s", Tobias brings up someone named Freddie Wilson while talking, prompting the other characters to say they "don't get that reference". This doubled as an in-joke about how some people thought the show's inability to gain mainstream appeal was caused by its numerous and sometimes obscure jokes about pop-culture and topical references.
Liz tells her writers not to use Krang from Teenage Mutant Ninja Turtles on sketches. "No one knows who Krang is! It would be a waste of time to talk about Krang on television! No more Krang!"
Another instance, this time when Liz is having a fake argument with Dot Com her pretend-boyfriend to make her new roommate move out (It Makes Sense in Context):
Dot Com: I feel ANGRY! Like Warren Moon must have felt back in 1995! Liz: As I have told you many times in our relationship, no one gets that reference.
In the House episode "Perils of Paranoia", House's team doubts that their Patient of the Week was a victim of chlorine gas poisoning. House, however, says that there still might be a toxin involved because "Arceus created a universe with three states of matter and 300 solid or liquid poisons that could cause his symptoms." Puzzled, Taub asks, "Arceus?" House casually replies, "Look it up."
In Father Ted, Ted makes a reference to the Jeff Bridges movie Fearless. When Dougal remarks that he hasn't seen it, Ted replies, "Not a lot of people have, Dougal, so it's probably a bad reference."
Mystery Science Theater 3000. The episode Gamera vs. Guiron has what is usually acknowledged as the most obscure joke in the entire show's history. Tom Servo makes a reference to head writer Mike Nelson's recent break-up with his girlfriend (and the fact that she took his computer keyboard when she left):
(a girl runs away from the camera) Tom Servo: Look out, Mike, she's got your keyboard! Joel: Huh? Tom Servo: Oh, it's obscure.
In Buffy the Vampire Slayer, "New Moon Rising", Buffy threatens to "pull a William Burroughs" on MacNamaranote Not a perfect analogy; the Burroughs case was William Telling gone wrong and Buffy would be deliberately shooting MacNamara, earning a lot of blank looks until Xander speculates she intends to "bore him to death with free prose."
Buffy: Was I the only one awake in English that day? I'll kill him.
In one episode of Whose Line Is It Anyway?, a game of Scenes from a Hat had the cast doing Redneck versions of Shakespeare plays. Wayne Brady enters and, in a thick hillbilly accent, recites a line from Two Gentlemen of Verona; when the audience fails to respond, he admonishes them with "Read a book, people!"
Mass Effect 3: If James talks Shepard into buying some fellow marines a round, the soldiers start a toast based on Robert Burns (that was also used in the videogame Return To Zork). Shepard's half is based on a Renegade Interrupt — hit it, and James admits he wasn't sure they'd know the line.
Yes, to understand this joke you need to know relativity and image processing theory. No, I am unrepentant.
In Dino Attack RPG, after Rockford grumbled about Dino Attack Team's code being blatant Star Wars references, Mur just remarked that he was glad it wasn't a much more obscure Firefly reference instead, much to Rockford's confusion.
Stuart Ashen has a recurring segment in his reviews, "Quincy: a caterpillar that sings obscure Beatles songs".
Spoony: Actually my first thought was that he kinda looks like Locklear from Betrayal at Krondor... Oh God... I just made a Betrayal at Krondor reference in Two-Thousand-and fucking-Eleven... I don't get out much...
Jew Wario: You lost me about five obscure references ago.
Animaniacs did a short where the Warner brothers (and the Warner sister) met Rasputin. They did a pun involving "Anastasia" getting mixed up with "anesthesia", and Dot said "Obscure Joke. Ask your parents." (This was years before that Don Bluth film came out.)
Family Guy mentioned Benjamin Disraeli in the episode "One If By Clam, Two If By Sea" to set up a Cutaway Gag. It cut to Disraeli working at his desk, when he suddenly glares at the camera and snaps "You don't even know who I am!"
Grandpa Simpson: I was lonelier than Estes Kefauver at a meeting of Murder Incorporated! (beat) That actually makes sense. Look it up!
"They Saved Lisa's Brain":
Lisa: (reading Comic Book Guy's shirt) "C:/DOS C:/DOS/RUN RUN/DOS/RUN". (laughs) Oh, only one person in a million would find that funny. Frink: Yes, we call that the "Dennis Miller Ratio".
An episode of Robot Chicken spoofed the ending to Sleepaway Camp. At the end of the skit, the director of Sleepaway Camp quickly shows up, ecstatic that someone remembered his movie and decided to spoof it.
On an episode of The Tick, a hand puppet compared The Tick to Achilles in his tent. When no one, even his ventriloquist, got it he said "The Illiad?" (looks around) "Homer?" (still no reaction) "READ A BOOK!!"
Bullwinkle: Twenty dollars!? That's antihistamine money! Rocky: Antihistamine money? Bullwinkle: Yes. It's not to be sneezed at. Get it? Not to be sneezed at? Rocky:I get it. Bullwinkle: Thousands won't!
In season 1, when Archer is training Cyril to be a field agent, he gives him a pistol (Chekhov 9mm) and a poison pen, both of which, he warns, go off for "basically no reason". Later, when a prostitute is accidentally killed by the pen, Cyril bemoans that he figured he have to watch out for the Chekhov's Gun. Archer dismisses this as "a facile argument" and Woodhouse chimes in that it's "also woefully esoteric".
In another episode, Archer makes a reference to Bartleby, The Scrivener, and is annoyed when no-one else gets it.
Admittedly Obscure Reference, Acknowledging The Obscure Reference, Lampshading The Obscure Reference, Lampshade The Obscure Reference