Chuck, the show, had dozens of shoutouts. Several per episode generally, to anything and everything geekworthy.
"Chuck Versus the Sandworm" had, in addition to all the Dune references you might expect, a lengthy visual shout out to "The O.C."
This is because the two shows share a creator/co-creator - Josh Schwartz. There is also an episode where they have to channel flick and identify TV shows as quickly as possible. It's very quick, but Morgan says "Season 2 of The O.C, a really underrated show" at one point.
"Sandworm" also mentioned Harry Tang's middle name is "Tiberius", the same as Captain Kirk's.
In "Chuck Versus the Sandworm," he asks (in reference to a hacker geek who escaped from a secure facility), "What's he going to do, hurt me with his mind?"
Likewise, Casey mutters "Shiny!" in another episode.
In "Chuck Vs. the Crown Victoria," Chuck comments, "Shiny," when he sees Casey waxing his car.
At one point, he states that Chuck is "damaging his calm."
In "Chuck versus the Fear Of Death," there's a low-key one when Casey is confronting Greta, where he says the doesn't care "what crew you were on."
The name Charles Bartowski is two letters different from renowned author Charles Bukowski. Hard to believe that this is a coincidence.
Sports references abound in Season Two:
The bad guy of "Chuck Versus the Break-Up" is named after outfielder Von Hayes.
In "Chuck Versus the Ex," Jill's boss is named Guy Lafleur which is also the name of a Hall of Fame hockey player.
In "Chuck Versus the DeLorean," a character uses the alias Guido Merkins, a QB in the NFL.
The second season has two shout-outs to Grosse Pointe Blank- Chuck makes a reference to Sarah fighting rebellion in Paraguay with a fork which sounds very similar to Martin's claim to have killed a president of Paraguay with this eating utensil. The next episode has Sarah being forced to go to her high school reunion as part of an assignment, which fits the plot of that film.
That selfsame episode, "Chuck Versus the Cougars," also contains a shout out to Risky Business with the side-plot at the Buy More mirroring that film fairly closely.
The second season opener has a shout out to Batman Begins, the messenger who attacks Casey uses the same weapon that Jonathon Crane uses to dispense his fear toxin.
In "Chuck Versus the Best Friend" when Jeff is trying to convince Lester to sing he directly quotes "Lose Yourself" by Eminem from the movie 8 Mile. "Look, if you had one shot, one opportunity to seize everything you ever wanted, one moment would you capture it, or just let it slip?"
Point of fact, the character Ben Lo Pan is actually played by James Hong, who played David Lo Pan in Big Trouble in Little China.
The Christmas 2008 episode contains a shout-out to Die Hard when Reginald VelJohnson guest stars as Sgt. Al Powell of the Burbank Police Department. There's also a shoutout to Groundhog Day with the hostage holder, "Ned Ryerson" (spelled differently on the show than in the movie).
Several shout-outs to Casablanca: "We'll always have Omaha." It's Ellie's favorite movie, as well.
"Chuck Versus the Undercover Lover" contains a bunch for Casablanca. Cynical lone wolf Casey reopens an old wound when he unexpectedly encounters his old flame Ilsa and finds that she's about to marry Victor, the movie plays in the background at the Buy More when Ilsa comes to meet Casey, and at the end, after Ilsa leaves on a plane, Chuck says, "I think this is the beginning of a beautiful friendship." (see Whole-Plot Reference below).
Chuck keeps the documents given to him by Orion hidden in an issue of Ex Machina.
On more than one occasion, the team has deployed a GLG-20 listening device, a shout out to Spies Like Us. Another such shout-out was when Chuck, pretending to be a doctor, had an extended "Doctor"-"Doctor" greeting with a villain doctor. Emmett Millbarge is a cross between the names of the two spies in the movie.
Lets face it, Spies Like Us is a frequent target of Chuck shoutouts.
"Chuck Versus Tom Sawyer," an episode about Missile Command and Rush also had a model of Mazinger Z visible in one scene. Sharper-eyed viewers will also be able to glimpse the back of a model of Ultraman in that same sequence.
The choreography during the final scene of "Chuck Versus the Ring" was largely lifted directly from The Matrix... this troper wasn't sure it was intentional until Chuck said "I know Kung Fu."
The scene of Chuck and Sarah shooting up the "First bank of Evil" in season 4 is similar to when Neo and Trinity rescued Morpheus.
The whole Morgan betraying Big Mike arc was a shout out to The Godfather. Right down to the dialogue;
Mike: I know it was you, Fredo Morgan. You broke my heart. You broke my heart. [to Emmett] I don't want anything to happen to him while Mom's alive I'm dating his mother.
In "Chuck Versus the Alma Mater," Casey quotes Firesign Theatre's "Nick Danger" sketch.
"Chuck Versus the Third Dimension" has possibly the geekiest one of all - an explosive labeled "IG-88", the serial number of an assassin robot who was only named in the Star WarsExpanded Universe.
When Sarah tells Chuck that she wants to make love to him to improve their cover, he swallows his coffee and remarks "Hot coffee!"
Issues of Knights of the Dinner Table are seen in Chuck's room. (The writer wrote in to the magazine itself once to point this fact out.)
Chuck's room has a poster for the imaginary "Yakuza Prep," originally found in the bedroom of Seth on The O.C. (Also created by Josh Schwartz)
In "Chuck Versus First Class", the vial of antidote is labeled "cordrazine", a fictional drug mentioned in both Star Trek and Mission Impossible.
Eagle-eyed viewers may recognize the museum in "Chuck Versus the Mask" as the Power Rangers' Command Center.
Y: The Last Man is featured throughout the show multiple times. Chuck has a Y poster in his bedroom, Devon is shown reading the first issue while waiting for Chuck to wake up, Chuck is reading it at the bar to lure Manoosh. He refers to it as, "The greatest literary contribution of our time." --clearly one of the writers is a fan.
There are even parallels in the stories. A loser-jokester guy unwittingly becomes the most important man in the world in one day, he has a sister in medicine, and a kick-ass spy watching his back.
In "Chuck Versus the Couch Lock", when one of the villains is going through the mailboxes in Chuck's appartment complex, it is revealed that Casey's neighbor is named Bauer. When 24 was still running the shows were indeed "neighbors," since both aired on Monday night.
Casey: I had them court-martialed. Of course they promptly escaped the maximum security stockade...
Chuck: ...to the Los Angeles Underground, where they survived as soldiers of fortune.
Chuck: Like the... A-Team. You never have... have you ever seen the A-Team?
Casey: I was the A-Team.
The funeral scene in the same episode also seems to reference this scene from the Cary Grant Audrey Hepburn movie Charade, where a group of four people agreed to steal gold when part of the OSS in World War II. When one of them died, the others at his funeral each tried to make sure he was dead. One sneezed on him, one held a mirror to his nose, and the other (in the exact same manner as Chuck) stuck a pin in him.
Nearly all of the Morgan scenes in "Chuck Versus the Leftovers" are references to Die Hard.
"Chuck Versus the Balcony" riffs on a famous scene from The Court Jester when trying to track a bottle of wine:
Morgan: Chuck, the '86 Chateau LeFranc is a peppery Pinot with a stable on the label and a stork on the cork.
Chuck: Copy that. Um, um, what, what, it was, it was a peppery Pinot, right? A peppery Pinot with a cork on the stork and a label on the stable?
Morgan: No, it's a... a stable on the label and a cork on the stork. Dude, it's--no, it's not. What did you just say?
(after tracking the contents of the bottle to a wine taster)
Chuck: Sir! Hi, sir, hi, excuse me. Um. I'm terribly sorry, but I believe there's been a mix-up downstairs, and you've received wrong glass of wine. That's actually the Burgundy from Bordeaux with the coil on the foil and the fork on the cork.
Dégustateur:Quoi? That does not make sense! They are both regions!This... is the peppery Pinot with the stable on the label and the stork on the cork!
"Chuck vs the Gobbler":
Sarah dying her hair from blonde to black after "going rogue" mirrors a similar change from Salt.
When Morgan, as the driver of Chuck's limo, is told to roll up the window, he replies "As you wish".
Emmett Millbarge screaming "NO TOUCHING!" at hoardes of customers. He's played by Tony Hale, most famous for his role on Arrested Development, where "No touching!" and variations thereof was one its many running gags.
The agent who gave Sarah a 49-B evaluation in season 2 is named Alex Forrest.nB
While Morgan investigated the construction going on in Castle, he posed as an agent. When one walked by him he pretended to be talking on his radio saying "No, they're just doing maintenance on Sector 7-G".
In "Chuck Versus the Frosted Tips", an Intersected Morgan evades tranq shots in a style not unlike Neo. Incidentally, Carrie-Ann Moss (who played Trinity in the movies) made an appearance in the episode.
In "Chuck Versus Bo" the X-13 memory erasure spray is often filmed in a manner highly reminiscent of neuralyzers from the Men in Black movies.
Moreover, the subplot of Jeff & Lester losing their memories of their recent predicaments is eerily similar to Memento, which, interestingly enough starred Carrie-Ann Moss (Gertrude Verbanski).
In the season 4 premiere, Morgan tries to flex while high-fiving Chuck in a shout out to Predator.
Morgan is carrying a Tyrell Corporation messenger bag when he meets Carina in "Chuck versus the Wookie".
At the end of "Chuck Versus the Kept Man", Casey is seen enjoying an episode of Downton Abbey.