These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alas, Poor Scrappy: Emmett in the Season 3 opener. An Asshole Victim for sure, and there are many who would quickly say that he deserved what he got, but others think it was a bit shocking given that, by and large, the Buy More crew was a separate world from the the Spy world and any danger to them was usually done for slapstick. The flippant way Casey covered it up while pressing the Reset Button was a bit callous, even for him.
Viciously subverted by Shaw seemingly getting over the reveal that Sarah killed his wife. Not so much.
In Ellie's case, this is a Justified Trope, as Chuck fixed her wedding rather quickly, and gave her the wedding she actually wanted, as opposed to the original, which was what her mother-in-law-to-be had arranged.
The CIA is forbidden to operate within US borders, but nearly all the missions Chuck and co. undertake are local. CIA operatives are actually called officers, CIA agents being native civilians who are cooperating with an officer, but Sarah is always referred to as Agent Walker instead of Officer Walker.
In "Chuck Versus the Muuurder" Chuck mentions that Lewis' World of Warcraft guild, "...brought down Deathwing, world first." However the episode aired eight months (almost to the day) before Deathwing was even killable.
Bryce Larkin, and quite honestly, anyone else who comes between Chuck & Sarah.
Ensemble Darkhorse: Carina was so popular after her first appearance that she later made return appearances in the third season episode "Chuck Versus the Three Words" and the fourth season episodes "Chuck Versus the CAT Squad" and "Chuck Versus the Cliffhanger".
The Director is quite popular among the fandom, despite only appearing in a handful of scenes in two episodes.
Cole Barker, while not a very prominent character, easily steals the episodes he's in thanks to being a charismatic, badass, Jerk with a Heart of Gold and Undying Loyalty. Being part of MI6 and a heroic British character after initially appearing to be a typical Evil Brit also help that.
Epileptic Trees: Everyone knows that Stephen Bartowski is Orion. Bryce also mentions that he befriended Chuck in college because he owed Orion a favor. Since Bryce is responsible for Chuck receiving the Intersect, is Orion the one really behind that part of the plot? Yeah, he denies it... but it seems HIGHLY SUSPICIOUS.
Executive Meddling: The third and fourth seasons have suffered somewhat from pacing issues, most of which can be attributed to the network holding off on ordering anything beyond the initial thirteen episodes until well after they are plotted out (which is why the thirteenth episodes of both seasons are wham episodes; they were also designed to be Grand Finales meant to end the show). The third season, while picked up, was given an additional six episodes as opposed to the standard nine, and as such required some condensation of the arc storyline into a shorter season. The fourth season has had the opposite treatment, where it has been given an additional eleven episodes as opposed to the standard nine. Oh, no.
While the awkward pacing might be bad news, one of the results is that Chuck & Sarah end up together at the end of "Chuck vs. The Other Guy", one of the show's 4 non-finalies. Viewers would be treated to Chuck and Sarah as an Battle Couple for the rest of the show's run.
Fans also christened Morgan "The Beard", which stuck.
Fan-Preferred Couple: Some fans definitely like the idea of Carina x Morgan. It also helps that she too has definitely warmed up to him, but alas, Morgan chose Alex over Carina and Anna.
Despite being happily married to Captain Awesome the fans tend to frequently ship Casey and Ellie.
"Funny Aneurysm" Moment: "Chuck Vs. the Third Dimension" has a scene where the rock star played by Dominic Monaghan is dedicating his upcoming concert in Nelson Mandela's memory, the joke being that Monaghan's character was oblivious to the fact that Mandela was still alive. However, Mandela passed away in December 2013.
Growing the Beard: The second season is a nice step above the entertaining but uneven first season.
This could partly be down to it getting cut short by the writer's strike. The third season is a step-up from the second season as well, in part because some of the story arc planned for Season 1 had to be stretched out across Season 2 as well.
Chuck's throwaway line to Ellie in the pilot that he'll get to work on a five year plan the next day. At the time, that's just plain funny because the next day he meets Sarah. It becomes Hilarious In Hindsight because the show ended after its fifth season.
Chuck's comment to Sarah, after she gives him a faked photograph of the two at Comic Con dressed as Han Solo & Slave!Leia in "Chuck Versus the Sand Worm",, that they've never actually been to Comic Con. Over the next few years, the Chuck panels at Comic Con would go on to be considered highlights of the event.
The first season featured Bryce Larkin engaging in a bit of Super Dickery, as he got Chuck kicked out of Stanford to protect him from being recruited into the CIA against his will. Matthew Bomer was not only a contender for playing the role of the the poster child for Super Dickery, but would go on to voice him in an animated film six years later.
Casey displays his Osama Bin Laden targets in an episode that aired one day after Bin Laden was killed.
Moral Event Horizon: Shaw trying to kill Sarah was his Start of Darkness. He crossed the MEH when he shoots Stephen Bartowski in order to cause Chuck enough emotional pain he'd be unable to flash and fight him head on.
On a slightly less severe one, Emmett secures his place as the most hatable man on the show who isn't a criminal when he manipulates Morgan into getting evidence of Big Mike's laziness to get him demoted so Emmett can take the store manager position. Its made worse by the fact that, not only did this involve abusing the trust Mike had in Morgan, but also the trust Mike had in Emmett himself. Given his general personality, this act shows that Emmett might actually be a complete sociopath.
In a somewhat hilarious coincidence, Shaw is played by Brandon Routh who came on board Superman Returns when Bryan Singer took over for Brett Ratner. Ratner's choice to play Clark Kent/Superman? Matthew Bomer (Bryce Larkin).
Another funny coincidence: In his first appearance, Routh says "I hate guns, but it pays to know how to use one." In the episode of White Collar airing the same week, Bomer's character says almost exactly the same line.
The Scrappy: It is very, very hard not to hate Milbarge.
Once again, Daniel Shaw. Or more specifically it was less the character than it was Brandon Routh's portrayal, as many fans found he had virtually no chemistry with the rest of the cast and was The Stoic to an extent in broke Willing Suspension of Disbelief. At least until his Face-Heel Turn, when Routh proved that no, he's not actually a robot.
Seasonal Rot: Fandom was split over whether season 3 was worse than season 2, but most agree that the fourth season isn't as fresh as the preceding two.
Sending Stuff To Save The Show: Success! Fans have sent Nerds candy to the network. In a variant, fans also rewarded product placement sponsor Subway by buying footlong sandwiches.
She Really Can Act: Nicole Ritchie's performance got this surprised reaction from many viewers.
Wangst: While not as guilty as other shows, the writers do tend to hit the "Chuck and Sarah can never be" chord a LOT. Until, of course, they are.
"Funny Aneurysm" Moment/Hilarious in Hindsight: In "Chuck Versus Agent X," an early scene shows Casey eagerly anticipating a visit to a Vegas gun range. He even brought his "fancy" targets: Osama bin Laden pictures. By pure coincidence, the episode aired the day after Osama bin Laden was announced dead. Because of the nature of YMMV, it can be either one of these for the viewer.
Magnificent Bastard: Sarah's dad. Conning his partners, which saved his life and included his daughter, out of 10 million dollars they helped him steal? Sure, that's pretty bastardly, but managing to pickpocket the Cuban Cigar he gave Casey as a token of celebration to the success of the con, and then immediately be seen smoking the cigar while he still smokes his own?' Now that's Magnificent.
Unfortunate Implications: The murderer who also bombed Castle in Chuck vs. the Muuurder is...yep, the generically terrorist-looking brown guy! Even after they lampshaded it mercilessly and seemed to be going in another direction entirely! Thought you had more class than that, show.
Played with in the same example. Damian, the villain, is often mistaken for an Islamic Terrorist due to his appearance - but is actually a Greek merc-for-hire.