Another reference from Trading Places; the classical score uses bits of the overture from The Marriage of Figaro, which, according to Wikipedia, “concerns the story of a servant who is wronged by his wealthy employer Count Almaviva, and takes his revenge by unraveling the count’s own machinations.”
The characters in Seinfeld constantly reference things that happened weeks, months, and even years ago. My favorite is the one in “The Bookstore” (E17, S 09), where Kramer tells a homeless guy who goes by the name of “Rusty,” “I once knew a horse named Rusty.”
“Rusty” was the horse in “The Rye” (E 11, S 07) to whom Kramer fed Beef-a-Reeno, thereby giving him unbearable flatulence.
Much of the background music in the Seinfeld episode “The Barber” was from Rossini’s The Barber of Seville.
In the same vein as the Cary Grant examples above, the running gag in Arsenic and Old Lace is that Jonathan Brewster, after his plastic surgery, looks like Boris Karloff (supposedly because Dr. Einstein operated on him while drunk, after seeing Frankenstein). The joke, of course, is that Boris Karloff DID play Jonathan on Broadway in Joseph Kesselring’s play.
They used the same line in the motion picture, which Karloff couldn’t be in (because he was still performing the role on Broadway), so it loses its bite when it’s said about Raymond Massey playing Jonathan (although Massey looked enough like Karloff that he could pull it off), but audiences who knew about the line could still appreciate it.
It certainly wasn’t obscure at the time, but it might be today. The last lines in the movie What’s up Doc (directed by Peter Bogdanovich and written – mostly – by Buck Henry) were exchanged between Ryan O’Neal and Barbara Streisand:
O’Neal: I’d like to say I’m sorry
Streisand: Being in love means never having to say you’re sorry.
(several beats of silence, during which Streisand bats her eyes)
O’Neal: That’s the stupidest thing I ever heard.
Of course, the line “Love means never having to say you’re sorry” was the signature line of Love Story, O’Neal’s breakout role. The long silence wasn’t in theaters, where the audience typically laughed throughout the eye-batting.
The last scene in High Plains Drifter is in a cemetery. Several of the tombstones have the names of the producers and directors of the spaghetti westerns that had made Clint Eastwood famous.
In Arrested Development, Henry Winkler played Barry Zuckerkorn, the Bluth family’s lawyer. In the third season, they fired Barry and replaced him with Bob Loblaw (one of the greatest character names in TV history, by the way) - played by Scott Baio.
This was a reference to Baio’s character Chachi essentially replacing the Fonz (Henry Winkler) in later seasons of Happy Days. The characters on Arrested Development even remark from time to time that Loblaw is a poor replacement for Zuckerkorn.
I had no idea he was Ken Tremendous. Loved that blog.
O’Neal: I’d like to say I’m sorry
Streisand: Being in love means never having to say you’re sorry.
Watching Barry Lyndon for the first time, I said the same thing when O’Neal apologized to Marisa Berenson for something.
The woman sitting next to me laughed and said “Right actor, wrong movie!” 
Not an obscure reference, but Rusty was Uncle Rico in Napolean Dynamite.
Archer is about 25% obscure references. Too much to explain, but watch Training Day for some great examples:
Archer - No, do not say the Chekhov gun, Cyril. That, sir, is a facile argument.
Woodhouse - Also woefully esoteric.
There’s also a scene where Zuckerkorn (Winkler) jumps over a shark on a pier, calling back to Fonzie jumping the shark, which coined the phrase.
One of my favorite Simpsons references came at the start of “Homer Simpson, This Is Your Wife” (2006), where they were watching CSI: Miami on TV:
[Horatio Caine and Frank Tripp are leaning over a fresh murder victim]
TRIPP: How a man could have murdered his wife if he was making a phone call from 3,000 miles away?!?
CAINE: Maybe he reached out … [Dramatically removes sunglasses] … and killed someone.
[Theme music blares]
This is, of course, a reference to the AT&T ads in the '70s and '80s: Reach out, reach out and touch someone! Reach out, reach out and just say “Hi!”…
(I had to explain this one to my daughter, who was six at the time. We both laughed at the CSI parody, but the AT&T joke went completely over her head.)
After the second season of Arrested Development almost 2/3 of the jokes in any given episode were inside jokes to references to past episodes. That’s part of the reason it never took off during its original run on Fox, and also why it also has a huge cult following.
There’s too many “brain bombs” to list for that series. One of my favorites is as follows:
There are continuous running gags about incest throughout the series. In one of the later seasons, Justin Bateman’s character (Michael Bluth) is at a bar and sees a cute girl that he attempts to pick up. The girl is played by Justine Bateman.
…Jason Bateman, 
,
The TV show St. Elsewhere did this a lot.
In one episode, Dr. Mark Craig, a surgeon played by William Daniels, has a temper tantrum and slams his fist into a wall, hurting it badly. He and his wife visit a surgeon who specializes in work on hands, and go to Philadephia to consult with him. Dr. and Mrs Craig are walking along and she asks him “Mark, why did we have to come to Philadelphia in the summer? It’s too damned hot” He starts singing “It’s hot as hell, in Philadel-phia.” That’s a line from a song in the musical 1776, in which Daniels plays John Adam.
Justine Bateman. 
One of the best references on St Elsewhere came when the hospital staff was grieving over the death of Dr Bobby Caldwell (played by Mark Harmon) from AIDS in California. IIRC, it was Ehrlich who explained to a new cast member “Some people thought he was the sexiest man alive.”
This was not long after People magazine declared Mark Harmon the sexiest man alive.
I’ve heard that on NCIS someone asked what David McCallum’s character looked like when he was younger and someone said “Illya Kuryakin” - who McCallum had played decades earlier.
In the awful Beverly Hillbillies movie that came out in the '90s, the Clampetts seek the help of a private investigator who turns out to be Barnaby Jones from the '70s.
I don’t remember if they ever referred to the PI by name, but he was of course played by Buddy Ebsen, who was both BJ in the '70s and the original Jed Clampett in the '60s.
My ex, who is Russian, saw the movie and naturally missed the joke completely. (Just like my daughter didn’t know that Barbara Billingsley in Airplane! was June Cleaver (Beaver’s mom) in the '50s and '60s. To her, she was just “the old woman who spoke Jive.”)
At a certain point, she says something and Jason l says, “Marry me.” Then there’s a pause and Jason says, “This is wrong on so many levels.”
Another favorite from the show was one time when George Michael walks dejectedly home. The background music plays “Christmas Time is Here” from A Charlie Brown Christmas and he passes a doghouse with a beagle lying on it.
MST3K is full of obscure references…blink and you’ll miss 'em.
There are several references to Who songs in Veronica Mars, including one to Pinball Wizard (“Lord of the Pi’s”/S8 E3) and another to Magic Bus (“Driver Ed”/S2 E2).