In the Arrested Development episode Public Relations, Jessie, the publicist, insults George Michael by calling him “Opie”. The narrator (Ron Howard, who played Opie) says “Jessie had gone too far, and she had best watch her mouth.”
Not a joke per se, but definitely an “inside” shout-out: In a first season episode of ST: TNG, the one with the whole planet full of plague victims who are really drug addicts. This was the last episode shot with Denise Crosby (the episode in which her character Tasha Yar died was already filmed, and this one was filmed out of chronological order.) Her character Tasha breaks the fourth wall and waves goodbye to the audience.
It occurs at the end of the episode: Picard & Crusher are leaving the cargo bay and entering the turbolift. They are clearly the focus of the shot, and Yar is way in the background, but if you look you can definitely see her wave.
He also said d’oh when he played a surgeon on Arrested Development.
There was an episode of Thrid Rock where the kids had to go to an emergency room. The shots, handheld camera and all, were directly stolen from ER, currently the #1 show on the air.
There were a couple where actors from other MTM shows were mistaken for their characters - Betty White was called “Sue Ann” by a man who thought that he was Mary Richards, and Tim Van Patten was called “Salami” (his character on The White Shadow) by an orderly - who was a character on The White Shadow himself (in one episode, he explains that he got a basketball scholarship to Boston College, only to blow out his knee and end any hopes of a basketball career).
When Lisa Kudrow returned to Mad About You, her character was asked where she had been, and she replied, “With friends.” (Yes, I am aware that her MAY character is Phoebe’s twin sister Ursula.)
There’s one that I am fairly certain is an inside joke - either that, or it’s an incredible coincidence; on ER, Dr. Green’s daughter’s first name is Rachel. Rachel Green is Jennifer Aniston’s character on Friends.
There was also an Andy Griffith mention by Howard.
Those are just shout-outs. Nobody from NCIS was in *Animal House *AFAIR.
There was an episode of Babylon 5, where Vir was discovered to be running an underground railroad to smuggle Narns off their home planet, and he had a line about how “they were brought here to Babylon 5 for medical attention, or sent elsewhere”
Vir was played by actor Stephen Furst, Elliot Alexrod in St Elsewhere
LOL. Makes me wish I’ve seen more of Firefly/Serenity than I have. I watch Castle all the time but I don’t always catch all the in-jokes.
That said, even I couldn’t miss these two: in the ep that was a nod to Star Trek, et al. Jonathon Frakes (the director) shows up in the opener to get his book signed, claiming he’s Castle’s ‘Number One’ fan.
And Castle’s throwaway line as they’re exiting the spaceship set, “ ’I’m a fan of good sci-fi. Star Trek. Battlestar. That Joss Whedon show…’ ” 
There is a joke in “Stargate SG-1” when informed that the tv show 'Wormhole X-Treme" that an alien from space living in Hollywood has been made into a movie. Teal’c asks “who makes movie from a TV show that was cancelled after three episodes?”. This is a joke as to how the putrid tv series
“Firefly” was turned into an even worse film “Serenity”. Fortunately we have been spared “Firefly” being revived into a 10 year TV series like “Wormhole X-treme” was.
On SouthLAnd a season or two back Marla Gibbs played a senile old lady. When Lydia the detective comes to see her about some sort of crime, Marla calls her Brenda, the name of her daughter on 227, who like Lydia, was played by Regina King.
[sup][sup][sub][sub](calling Firefly putrid should be a bannable offense)[/sub][/sub][/sup][/sup]
Another Howie Mandel joke: Fiscus is recuperating after being shot. To cheer him up, Elliot and Luther (I think) march into the room and stand at the foot of his bed. Elliot says:
“We’d like to give you A BIG HAND!” [They try to blow up rubber gloves and fail miserably. Dejected, Elliot says] “Hmph! It worked fine on TV…”
(Mandel’s stand-up act included placing a latex glove over his head and inflating it by blowing through his nose, the fingers of the glove extending above his head like a cockscomb.)
Thought of another one.
In the British TV series The Avengers, at one time Steed had an assistant named Cathy Gale (played by Honor Blackman). She left the show and was replaced by Emma Peel (played by Diana Rigg).
In the episode Too Many Christmas Trees Steed is looking though some mail and picks up a postcard, saying “Ah, a postcard from Ms. Gale!” He then flips it over and says, somewhat quizzically, “I wonder what she’s doing in Fort Knox?”
Honor Blackman had left the show to play Pussy Galore in Goldfinger which, of course, took place in Fort Knox.
In a later New Avengers episode, Steed and Gambit solve the crisis of the week by releasing several crates of cats into a building. (Don’t ask.) Later they go in and see cats everywhere. They look around and say…
Gambit: “Pussy”
Steed: “Galore”
Had to add a really good one from Psych last night. Parminder Nagra (star of “Bend It Like Beckham”) is Gus’s new love interest and in the cold open they have them playing soccer at a picnic. Gus is talking trash while goalkeeping before Parminder shoots a great shot right past Gus’s head.
Bump.
I thought that there was a more recent thread with inside joke/older role references in TV shows, but this is what I googled up. In a recent episode of Stan against Evil, Stan (played by John C. McGinley) is in the hospital, being treated by–a Doctor Cox. And Stan tells him that when he finds a certain person to “call him a girl’s name”.