On Babylon 5, security chief Michael Garibaldi is a huge Looney Tunes fan. Unfortunetly, the subtlties of Daffy Duck are apparently lost on the Mimbari.
On “NCSI,” someone asked Gibbs what Ducky looked like when he was young? “Like Ilya Kuryakin.” So obviously The Man from U.N.C.L.E. exists in their universe.
Meet the Press aired in Homicide: Life on the Street 's universe (and by extension the entire Law & Order universe). NBC’s Tim Russert and Lt. Megan Russert of the Baltimore P.D. were cousins.
Felicity was shown in the Buffy 'verse. Xander said once that a person had “Gone all Felicity” with her hair, meaning that that person had had all her hair cut off.
Once again on “the Simpsons” - Bleeding Gums Murphy made an appearance on “the Cosby Show” as the fifth grandfather to the Huxtable kids.
Littlest Huxtable: That’s the fifth grandfather we’ve met.
Cliff: Yeah, but this grandfather is a famous old-time jazz musicians.
Littlest Huxtable: But ALL our grandparents are famous old-time jazz musicians.
South Park also exists in the universe of The Simpsons.
The other news network seen often in 24 is CNB, which based on the logo is supposed to be CNN. (I know it doesn’t exist in our world, but I’m just pointing out there’s more than one news network on 24.)
Presumably, The Nanny exists in the universe of The Nanny. In one of the final episodes, Fran Drescher’s character met Fran Drescher in a hotel. Fran the actress reminded Fran the nanny to watch the final episode of the series.
Now that I think about it, the only one who was really dismayed was Butters. I don’t think anyone else in South Park has a stash of evil plans (except maybe Cartman).
OOH! Got a great one!:
On one episode of The A-Team, Face is at Universal Studios theme park and watches a guy in a Cylon costume walk by. Though as far as I know nobody ever commented on his remarkable resemblence to actor Dirk Benedict.
In one episode of The X-Files, Mulder and Scully went undercover as a suburban married couple named Rob and Laura Petrie (I think Mulder chose the names), so presumably The Dick Van Dyke Show exists in that universe.
Porn.
One reference, and one non-reference.
Reference: On Seinfeld, Kramer suffered from seizures whenever he heard Mary Hart’s voice on Entertainment Tonight.
Non-reference: On an early episode of Friends, some of the ER docs make a guest appearance, playing doctors, but they are not the same characters as on ER. I guess a writer actually cared about continuity (given that Friends was set in NYC, and ER in Chicago.
Sua
On CSI-NY, a reporter for Entertainment Tonight was covering the fashion show with the dead model with the tiny titties. (Just caught it on the remote flyby…)
Cartman doesn’t need a stash of plans, every thought he has is basically evil. 
Jim
Herman’s Head existed in the reality of The Simpsons.
A series called Blondie (same as the one in the funny papers) once featured Jim Backus as Mr. Dithers. At least once, he was seen watching Gilligan’s Island.
Roseanne once had an episode where, during the closing credits, Dan and Roseanne watch Roseanne, on Spanish language television
Well, in the episode where Stewie is trying to stop Lois and Peter from conceiving another child, Stewie comments after learning that Peter’s pulse has increased, “My God! Either he’s watching ‘Batman,’ or they’re doing the do!”
It then cuts to Peter laying on the bed, and the Batman TV show theme is playing.
There’s another bit where Peter is talking about how bad it was when Lois was pregnant, and it cuts to him laying on the bed, watching TV. Lois is in the bathroom, throwing up. Peter turns up the volume, and the theme song to Three’s Company is playing.
“Yeah, but Scully’s the chick, right?”
You are my new hero.
Babylon 5 exists in the Buffy universe - Xander has a set of commemorative plates. I think they’re referenced in the episode where he is moving out of his parents’ basement. The Twilight Zone must also exist, as Dawn summarises the lessons she’s learnt from Buffy as, “You never know what’s coming, the stake is not the power, and ‘To Serve Man’ is a cookbook.” Heh.
Twin Peaks featured a fictional soap opera called Invitation To Love.
Not to mention, Rose is revealed in one episode to be a walking encyclopedia of Miami Vice trivia, even getting hit on by a Sonny Crockett wannabe vice cop.
In South Park, it’s obvious from Mr. Garrison’s lessons that a number of real TV shows exist in that universe, as well as other sources
Off the top of my head…
-Simon and Simon.
-The Facts of Life.
-Sam Adams commericals(okay, not a show, but a real brand).
-Barneby Jones.
-American Idol.
-The Contender.
-The O’Reilly Factor.
-Star Trek has been mentioned a number of times.
-Crossing over with John Edward(at least until the aliens took him away).
-A number of real movies(Independence Day, the Goonies, The Passon of the Christ, Rob Schenieder movies, allusions to )
-Ike was watching some news show in one episode(“Terrence and Phillip Trailor”) that I assume was real.
I’m sure there’s more.
In American Dad, the show 24 obviously exists in that universe.
More Family Guy:
VH1’s Behind the Music.
To be fair, Enterprise is still the name of a very prominent and actively serving US Navy ship (or at least, I assume it is since the show doesn’t say otherwise and it more or less takes place in the “Real World” glancing at the fourth wall in my room), so the name wasn’t available.
Other than that, Daffy existing within B5 has been mentioned (One character describes him as “The Human God of Frustration”). Micheal Garibaldi apparantly has a Daffy Duck design painted on his Starfury in the 5th season of the show.
On one episode of B5, Captain Sheridan makes a passing reference to Lucy and Ethel from “I Love Lucy”
Adding to the B5 on Buffy bit, Jonathan apparantly owns or used to own some Babylon 5 novels, which Warren and Andrew colored with a highlighter at some point. (having had one of my Babylon 5 novels vandalized by classmates in high school, I can understand why they’d be worried that Jonathan would turn on them).
Also on Buffy, Trogdor the Burninator exists as part of a pen-and-paper RPG, though it’s unclear if the RPG is a HomeStar Runner RPG or not.
Oh, and in addition to Star Trek in general being referenced on Buffy, Star Trek: Enterprise is specifically mentioned on numerous occasions in the 6th and 7th seasons (“Ahh… Captain Archer…”)
Angel has made a number of references to Batman (apparantly it was a running joke early on)
Star Wars exists both on StarGate SG1 and The Pretender (Teal’C and whatever the name of the pretender guy on the Pretender both get to watch the movies fairly late in life).
The anime Nadesico featured clips from a then-fictional anime called Gekigangar III, which was later made into an OVA by the company that made Nadesico.
Superman is mentioned in an episode of The Mighty Morphin Power Rangers, but it’s not made clear if he is fictional or not on that show.
On a tangentially related note, does anybody remember the old days when all the different computer games referred to eachother or co-existed (ie: Crusader, Wing Commander, and Ultima VII are all in the same universe, Brittania apparantly being located on a planet occasionally visited by the Kilrathi, System Shock and BioForge are the basis of a couple of movies reviewed in the TCS Victory’s newsletter that came with Wing Commander III)
Considering that Andrew is seen on Angel wearing a Strongbad T-shirt, I think it’s more likely he’s just one of these terrible GM’s that incorporates in-jokes from pop-culture into his adventures. (I can say this since I once was such a GM, giggling like a madman as my players faced off against Grandpa Munster. Thankfully I grew out of it.)