In jokes slipped onto TV shows

Family Guy has possibly one of the most obvious in jokes ever, Adam West as Mayor Adam West who has frequent delusions about crime fighting etc, and being prepared for things (a'la Batman/Batbelt).

After the series restarted they had a scene where Peter is saying to Louis that the series is cancelled and she asks if there is any chance of it coming back, and he lists the programmes that would have to be cancelled for that to happen (a long list of shows that were cancelled by the network between the end of the previous series of FG and it's return).

A few Anime in jokes/references
In Gunbuster (Made by Gainax who are major anime fans), there are various posters, one being Totoro above the main characters bed.
One of the secondary (American iirc) characters is named after an American who was visiting on a licensing trip.
The method of entering FTL travel was called a Tannhauser Gate, after a reference in Blade Runner.

On a related note in Star Trek The Next Generation there is a species of sentient whales called Takaya's Whales that are named after the main character in Gunbuster (which had whales/dolphins serving as navigation crew in one episode), I don't think they were ever mentioned specifically on screen but there were references to "Cetacean ops" in the TV series and were on some Galaxy class ships (I think they are named specifically in one of the books).
Apparently one of the writers is/was a big fan of Gubuster.
Talking of ST:TNG - apparently a lot of the consoie text was jokes/references to cast and crew from memory, but was rarely if ever readable.

From memory in Serenity there are several boxes with the label "Do not dispose of, reusable" which is apparently a reference to the fact that (from memory) despite Whedon asking/warning that the set/props should not be disposed of after Firefly got cancelled, the props were disposed of (so they had to rebuild much of the set and many of the props for the film).

If you just want references to other shows, then the opening to Daicon III and IV in 81 and 83 (big Japanese sci-fi con), an animation made by several students who went on to found the Animation Studio Gainax, would probably be very hard to beat.
It's got hundreRAB of references to everything from Metropolis, Conan and Forbidden Planet, through to Star Wars and Aliens, with pretty much every major Sci-fi series/film/comic/anime of the time represented (one sequence has the main character flying over a crowd of characters, in another she's fighting Darth Vader, Godzilla, and in another the Enterprise is blown up alongside the Yamamoto).
I tried counting them once, and got to about 200 characters/ships I recognised (not including the fact that the main character was wearing a red bunny girl outfit, and in a flying Daicon radish), before I gave up. For Star Wars alone there was Darth Vader, Storm Troopers, the Deathstar, Yoda, Tie fighters and I think a Star Destroyer.
 
I didn't get that joke until I knew that Lisa Kudrow was in Mad About You.

There's a clip of Kramer from Seinfeld in Mad About You, as he was renting his flat from Paul or someone from MAY, and referring to the guy who lived opposite (Seinfeld) as he's just a comedian. More of a cross over than an in joke.
 
Then there is the episode where the young brother goes to a shrink as an grown up, played by John Goodman. Apparently the changing sister has messed with his mind. He sits rocking backwarRAB and forwarRAB muttering 'they say she's the same but she's not the same'.
 
I thought I was the only person who got that! Even on the favourite quotes on the NCIS site no one has mentioned that. I thought it was very clever.
 
Two I noticed from House (the first is well known):

In one episode, Wilson is flicking through the programmes recorded on House's TIVO. One of the recordings is Blackadder.

In another, House enters Cuddy's office and she asks him if he's come to argue. He says he'd need room 12A for that. It's a reference to Monty Python's Argument Clinic sketch.
 
"Chuck" managed a double in joke when Hannah (played by Kristin Kreuk) says how hanRABome Daniel Shaw is (played by Brandon Routh) and Chuck says something along the lines of "Well, if you go for that Superman type".

Not only did Kreuk play Lana Lang in Smallville (thus in a previous life she did go for the Superman type) but Routh of course played Superman in the film "Superman Returns".
 
There is a number of in jokes that feature in "The X Files"

Season 1

"The Jersey Devil" - In the autopsy report on "Jane Doe", the name of the coroner is K.H.Hawryliw. Ken Hawryliw is the prop master on the show.

Season 2

"Die Hand Die Verletzt" - The message left by the devilish teacher for Mulder and Scully, 'Good-bye - It's been nice working with you' also served as Morgan and Wong's farewell to the cast and crew, since this was their last episode with the show until they came back for a brief stint in season four.

Season3

"Piper Maru" - The name of the episode is also the name of Gillian Anderson's daughter.
 
I don't know if it's been mentioned yet, but in Supernatural, the brothers often reference characters from other TV shows and I believe singers as their alias's.
Almost every episode is also named as a reference to either songs or film.
 
It made me laugh when I saw it, as I used to be a big man from uncle fan when I was younger (and the first time I saw Ducky I thought to myself "that's whatshisname from Uncle").
 
In a recent episode of A town called Eureka, they all start hallucinating people from their past with whom they have unresolved issues. One of them asks Dr Grant, played by James Callis, who he sees and he replies - A tall leggy blonde in a red dress! - A nice nod back to his BSG days.
 
The Board of CH wanted to market/rbrand the hospital. The whole episode featured various staff members being filmed. At the end we saw the new advert video - it was done in the style of the ER opening credits :D:D:D

In an episode of StE, three doctors went for a drink after work - to the Cheers bar (both are in the same town) :D:D:D
 
In an episode of The A team ,Faceman (Dirk Benedict) is on the Universal Studio lot when a Cylon from Battlestar Calactica walks by causing Face to do a double take. Of course Dirk played Starbuck in Battlestar
 
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