Lampshaded the Obscure Reference

"Welcome to Julie Taymor's Playhouse. [beat] Like five of you got that, but the five of you who got it are gonna be laughing."

—Doug Walker during his tour of Austria.

When a reference or Shout-Out is made, and it's acknowledged In-Universe to be obscure.

This isn't done all the time, because references tend to be subtle if they are obscure, so that those that don't get them can just enjoy the show. Doing it once in a while can give the audience a bit of curiosity about the reference, but not slow down the show with them wondering about every one.

A Sub-Trope of Genius Bonus.

Compare Pop Cultural Osmosis Failure, Shown Their Work, Late to the Punchline.

Contrast Small Reference Pools.

Not to be confused with characters not getting a commonly known thing.

Examples of Lampshaded the Obscure Reference include:

Live-Action TV

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.
Played with in an episode of The Middleman, where Middleman '69 (who has been in cryonic stasis for the past four decades) makes a Star Trek reference and notes the unlikeliness of Wendy getting it.
On 30 Rock, 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!"

Recorded and Stand Up Comedy

Dennis Miller constantly uses obscure pop culture references in his stand-up routine. He occasionally mentions that he's doing so and that many of the people watching won't get them.

Web Original

Yu-Gi-Oh!: The Abridged Series did a scene which referenced Rickroll, The Incredible Hulk and The Legend of Zelda. Tea said she was leaving due to getting annoyed by all the obscure references.
Stuart Ashen has a recurring segment in his reviews, "Quincy: a caterpillar that sings obscure Beatles songs".
Hbi2k calls some of his jokes "2 percenters" based on how much he thinks his viewers get them.
In Dragon Ball 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."
The Spoony One occasionally succumbs to this:

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...

- He also feels the need to explain to his younger viewers what things like floppy disks and BBS were.
In Episode 11 of Teen Titans Abridged, Robin wondered who declared it obscure reference day.
In The Randomverse's Ways to Screw Up The Avengers Movie, it's mentioned that the villain is "not Loki, but Sean Connery and his weather machine". Deadpool appears to say "Obscure reference for the win!"
Psycomedia does this, often via the use of Venn diagram. Often involving the Star Wars Expanded Universe in one of the host's case.
In episode 13 Code MENT, Lelouch calls himself "a regular Dick Tracey." Suzaku says back, "Five people left on the planet know who that is and I'm not one of them!"
Linkara of Atop the Fourth Wall does this once in a while.

"My thanks to the three people who get that joke."

Web Comics

One The Order of the Stick comic ends with characters being torn apart by a giant Ollie of Kukla, Fran and Ollie fame. The comic's title was "Ask Your Grandparents".
The commentary to Irregular Webcomic strip #617:

"Yes, to understand this joke you need to know relativity and image processing theory. No, I am unrepentant."

Western Animation

Animaniacs did a short where the Warner brothers (and the Warner sister) met Rasputin. They did a pun between "Anastasia" and "anesthesia", and Dot said "Obscure Joke. Ask your parents."
Archer: the titular Archer frequently admonishes his colleagues to "Read a book", owing to the obscurity of his references.
- Several instances in season 9 Danger Island occur:
  - Episode 5 - Archer says "insert name of obscure cartographer" and Crackers replies "Henrik Hondius".
  - Episode 6 - Archer says "nobody gets that" (about a Frisky Dingo reference).
  - Episode 7 - Noah says "they won't get the reference" with regards to the cannibals. The audience might, but the cannibals definitely wouldn't, lacking any filmic references whatsoever.
    - It very much depends on what is meant by obscure - to younger audiences, most of the references will be obscure, but attention is definitely called to references which are believed to be obscure for even the oldest audience members.
The Batman: The Brave And The Bold series finale had a character from The DCU appear for the first time.

"Ambush Bug? You're a pretty obscure hero, even for this show."

Family Guy mentioned Benjamin Disraeli to set up a Cutaway Gag. It cut to Disraeli just looking at the camera and snapping that the viewers didn't have any idea who he was.
Rick and Morty: this trope is subverted in Season 2 Episode 1 ("A Rickle In Time"):

Rick: Man, that guy is the "Redgrin Grumble" to pretending he knows what's going on.
Summer and Morty: Laugh
Rick: You like that "Redgrin Grumble" reference? Well guess what? I made him up. You really are your father's children. Think for yourselves. Don't be sheep.

The Simpsons has done this a few times.

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. The director of Sleepaway Camp quickly showed up and was amazed that anyone would decide to spoof the movie, let alone know the movie even existed.
A joke from Rocky and Bullwinkle:

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!

On an episode of The Tick (animation), 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!!"