Adam Baldwin is playing a patriotic version of his Firefly character, without the greed, the beard, and the disregard for authority. It's also hard to ignore that their initials are identical, which may or may not be intentional.
He also threatened to remove Chuck's "man parts"; in Firefly Jayne once threatened to show River his "man parts" if she kept insinuating the femininity of his name.
In "Chuck Versus the Fear of Death", Casey asks Greta what kind of "crew" she used to be on.
There's also a mention of Full Metal Jacket. Animal Mother's line "Flush out your headgear, new guy." was also used by Casey at one point.
The first thing Scott Bakula says to Ellie? "Oh boy."
Emmett yelling "No touching!" at the hordes of Tyler Martin fans.
Speaking of Tyler Martin, he's pretty much what Charlie might have become if Locke hadn't helped him kick the drug habit.
In "Chuck Versus the Three Words," Morgan says that Carina is not some girl, but "basically a Swedish supermodel." Which is exactly what Mini Anden is in real life. (You may have seen her as the former face of Armani Code.)
Brandon Routh as Agent Shaw has donned glasses that look suspiciously like ones Clark Kent would wear.
In "Chuck Versus First Class," Hannah sees a character played by Stone Cold Steve Austin and tries to guess his profession— "A professional wrestler, maybe?"
"Chuck Versus the Anniversary" - Harry Dean Stanton as a Repo Man and Dolph Lundgren dropping several of his Rocky IV lines.
"Chuck Versus the Cubic Z" includes an Actor Allusion between two of its guest stars, as Stacy Keibler and Stone Cold Steve Austin have a brief reprise match.
Volkoff, as played by Timothy Dalton, has one. As it turns out, he once worked for MI 6.
Of course, they couldn't have Carrie-Anne Moss as a guest star and not feature at least one Bullet Time scene. (It happens in "Chuck Versus the Frosted Tips.")
In "Chuck Versus the Hack Off" a scene featuring Carrie-Anne Moss is segued into a laptop running a Matrixcode screen saver.
Celebrity Paradox: The James Bond franchise as well as shows like The O.C. and Smallville all exist in the Chuck universe yet they never notice the likes of Rachel Bilson, Kristin Kreuk and Timothy Dalton walking amongst them.
Perhaps the biggest: Chuck & Morgan are huge Star Wars fans & Casey's familiar enough with the series to torture Morgan by having him watch The Phantom Menace first & then spoiling that Vader's the father of Luke & Leia, but none of them notice that they're stealing a vase from Luke freakin' Skywalker at the start of season 5.
You can't learn anything about being a spy from Chevy Chase, even if he was Roark
Which makes Chuck's TRON poster all the more interesting.
Chuck has to battle noted HITG Richard Burgi (The Sentinel, Desperate Housewives, 24) to save Sarah. He's also the guy who insulted Jayne and his cunning hat. ("That hat makes you look like an idiot.")
Green Arrow needed protecting from his brother in "Chuck Versus the Bearded Bandit". Guess it wasn't a job for Superman...
Anyone paying attention to NBC's advertising knew that Abed was going to show up in "Chuck Versus the Hack-off." Not touted at all? Shirley, as a Buy More greenshirt with the hots for him.
Keeping with Community references, the same episode features Kick-Puncher as a prison inmate.
Casey Hendershot, Deadliest Warrior expert, appears twice as a mook. An Iranian villain from "Chuck vs. The A-Team" was (ironically) the lead IDF simulation actor.
Apparently Devon (Captain Awesome) was supposed to be a limited character who was supposed to turn out to be an enemy operative towards the end of season one. However his popularity led to the idea being dropped and Awesome becoming a series regular. The idea was recycled into Jill and re-recycled into an arc in season 3 where The Ring thinks Devon is the resident spy in the Bartowski family.
According to a discussion Alan Sepinwall had with the creators, they were originally going to try and hire Chuck Norris to play a major villain (most likely Leader from "Chuck Versus the Gravitron") in an episode that could only be titled "Chuck Versus Chuck."
You Look Familiar: The actor who played Yuri the Gobbler had also played one of La Ciudad's goons.