A meta example is the tribute to the fans at Comic Con, who ran the most effective Save Our Show campaign ever: They essentially bribed one of the main sponsors (Subway) into backing the show by buying so many sandwiches.
The end of the "Chuck Versus the Alma Mater," when we find out why Bryce got Chuck kicked out of Stanford.
Bryce: Chuck's a good person. He's got too much heart for this kind of work. He's no operative. You can't put him out in the field! He won't survive! Fleming: The Agency isn't going to let go of a recruit this promising! The amount of information he can retain? Bryce: They're not gonna give him a choice? Fleming: He's in no matter what. Bryce: ...if he cheated, on the exam, copied all the answers... that would invalidate all the results, wouldn't it?
Much of "Chuck Versus The Truth", what with characters from Chuck's personal life being put in serious danger for the first time, and the ending when it is revealed that Sarah had been trained to withstand Sodium Penthothal, and as such did have genuine feelings for Chuck though she denied them to him when supposedly under the influence of the truth serum.
In "Chuck Versus The Nemesis", Bryce is telling them how he is here. He reveals that even when he was this close to being clinically dead, he made himself a target by saying he was the Intersect instead of Chuck. True, it could be argued he knew then that they would have to keep him alive, but from the flashback we know he was pretty out of it and still his first instinct was to protect his friend.
In "Chuck Versus the Seduction", Chuck receives advise on how to seduce a villainess from Roan Montgomery. Roan belittles Chuck's natural approach towards women, favoring his own more traditional, chauvinistic, heavily-reliant-on alcohol methods. Sarah is visibly annoyed, and suggests that Chuck just be himself and rely on his own natural charm and wit to get results. "It worked on me." she unhesitatingly encourages. The formula for success turns out to be a hybrid between the two sets of advice
In "Chuck Versus the Cougars", Chuck spends a good chunk of the episode pestering Sarah for information about her high school years. Towards the end:
Sarah: "Okay, fine. I'll answer one question about my past; you've earned that much." Chuck: (after contemplating it) "No thanks. I don't need to know more about who you were. 'Cause as much as you don't think so, I know who you are: A girl I'd like to share a cheeseburger with."
Then they do share that cheeseburger, and it's adorable.
Morgan helping Lester fix Big Mike's fish because he wants Lester to know that people are good at heart.
"Chuck Versus the Best Friend:"
Chuck's whole "best friend" speech to Sarah:
Chuck: Look, Sarah, I don't have parents. I mean, not really. I know I don't talk about it, because that's just the way that things are now. But it wasn't always this way. Morgan was there the first day that my mom took off. He didn't say much, because, honestly, what is a fifth grader supposed to say? But we sat there and split a cherry cheesecake and played Legend of Zelda all night long. And my dad, that's a whole other story, but Morgan was there for that, too. Morgan is more than just my best friend: he's my family. Before you got here, and long after you've gone, Morgan is my family.
Pretty much entire end of the episode, especially considering it was scored to the Jeffster! rendition of Africa, starting off with Lester overcoming his fear of performing in front of his crowd to help his best friend achieve his dream. It then cuts to Sarah apologizing to Chuck about her dismissiveness when it came to Chuck's relationship with Morgan.
Sarah: I just don't really have anyone in my life like that, who cares about me. Chuck: (gazing intently at Sarah) Yeah, you do.
Closes with Chuck and Sarah holding hands. Made of Awwwwwwwwwww.
"Chuck Versus the Broken Heart:"
Sarah is removed from Team Bartowski when her superiors decide that her feelings for Chuck make her a liability. Casey spends most of the episode lusting after his very attractive new partner, who even likes guns as much as he does, only to dismiss her entirely when she insults Sarah.
Casey: You know, Forrest, I was gonna say earlier: I disagree with your assessment. Forrest: About what? Casey: Walker. She's a pro. Not only that, she's the best damn partner I ever had.
Later in the same episode, as Chuck makes his case that Sarah should be reinstated:
Chuck: Wait, General. I'm sorry, but isn't the most important part of being my handler making sure that I stay alive? Sarah: It's okay, Chuck. Casey: (To Sarah) No. It's not. (To the general) Let him finish.
"Chuck Versus the Colonel:"
Sarah decides to go against orders to help Chuck find his father
And for that matter, later on Casey catches up with them. It's a tense Mexican Standoff, Sarah has a gun on him and he has a gun on Chuck, when...
Casey: You made three crucial mistakes, Bartowski. You didn't realize you were being trailed for the last half-hour, you didn't bring nearly enough firepower, and you didn't ask me to join! (lowers gun) Chuck, slightly dumbfounded: ...C-Casey, would you like to help us rescue my father? Casey: I think your father has served his country honorably and deserves to attend his daughter's wedding.
"Chuck Versus the Ring:"
As Chuck and Sarah slow dance at Ellie and Awesome's wedding reception:
Chuck: You belong out there, saving the world. I'm just... I'm just not that guy. Sarah: How many times do you have to be a hero to realize that you are that guy?
Earlier when Fulcrum is about to execute Chuck, Bryce, and Sarah. And none other than Colonel John Casey parachutes in with his team and completely lays waste to all of them. Chuck, in shock, can only stare open-mouthed at Casey who deadpans "You rang." Awesome, yes obviously. But heartwarming because Casey has always been dismissive of Chuck, but he absolutely meant it when he gave Chuck his number and told him to call if he were ever in trouble.
When most people find out that they're about to die because their closest friend has been keeping a secret from them for almost 3 years, most would, at the very least, suffer a BSOD. What does Morgan do when he learns the truth?
Morgan: This is the BEST news I've ever heard! ...Dude, you are TOTALLY re-hired as my best friend!
And furthermore, what's his sole concern as he's about to die? He just wants to hear about the cool stuff that his friend's been doing in saving the world.
"Chuck Versus the Tic Tac:"
Chuck and Sarah go to bat for Casey, in a scene echoing Chuck's conversation with Sarah in "Chuck versus the Cougars:"
Casey: "You could be charged with treason. Hell, you didn't even know I was Alex Coburn until today." Chuck: "I don't care who you were. I know who you are. And you're not in this alone."
Again in "Chuck Versus the Tic Tac" when Sarah and Chuck are planning to break Casey out of prison
Sarah: "If we do this and we get caught, we're going to be tried for treason and you're going to lose everything and you'll never get a chance to be a real spy. Is that what you want?" Chuck: "It's Casey." Sarah: "I was hoping you'd say that."
Also, when Colonel James Keller tells Casey "Always have someone watching your back," the scene cuts to Sarah. This is a long way from the Casey in "Chuck Versus the Sensei" who only let his partner join him when she put a knife to his throat. The whole episode was really about how close the three members of Team Bartowski had become.
"Chuck Versus the Other Guy:"
We'll start with Casey telling Sarah the truth about the red test.
Walker: Casey? Thank you. Casey: Have a nice life, Walker.
Shortly after, there's the scene immediately following Chuck's drunken gaming:
"Chuck Versus The Honeymooners" is more like a Crowning Episode of Heartwarming as practically every moment in the episode is a Crowning Moment of Heartwarming. In particular, though, there's General Beckman's reaction to learning that Chuck and Sarah are officially together, indicating that she too ships it.
Beckman: I must caution you that allowing your private life to interfere with your professional one can be dangerous. But, off the record, it's about damn time.
In "Chuck Versus The Tooth," the entire exchange with Dr. Dreyfus:
Sarah: No, you don't understand. He's not like other people. He is... incredibly special. Dr. Dreyfus: Especially to you, I gather. Sarah: He needs to be okay. I - I need him to be okay. I'd like to go to the hospital tonight to talk to him. Try to figure this out. Help him somehow. Please...I love him. Dr. Dreyfus: Ever tell him that? Sarah: Please, Doctor, I am begging you. Dr. Dreyfus: You're not the only one. (Pulls back the door to reveal Casey is there too.)
The latter half of "Chuck Versus The Subway" and the entirety of "Chuck Versus The Ring, Part II" is this when it's not being Crowning Moment of Awesome:
In "Chuck Versus the Subway", after Shaw has been informed that Chuck & Orion have found the Ring base
Casey: Don't know when it happened, but our boy became a man. Bartowski's a spy. You picked a good one, Walker. Finally.
There's also a quieter one when Morgan says to Awesome that Alex is "one of us", just moments after meeting her because he knows that he could trust Casey's word and the word of his daughter without hesitation.
In "Chuck Versus the Ring, Part II," after Chuck refuses to kill Shaw.
Shaw: That's what makes you weak. Sarah: (knocks him out) No, that's what makes you great."
"Chuck Versus the Anniversary:"
Casey's complete lack of hesitation when Chuck asks if he'll help him find his mother. He even says he's only annoyed Chuck didn't ask sooner.
Chuck's reaction when he learns about Ellie's pregnancy.
"Chuck Versus the Suitcase:"
Morgan telling Casey that he'll never be a part of his daughter Alex's life if he never tries, after Casey claiming he just doesn't fit in. Not really a CMOH, but it comes at the end of the episode, when we see Casey taking Morgan's advice and calling his daughter.
Chuck discovering that for all the issues Sarah has with unpacking, she keeps a photograph of the two of them in the titular suitcase.
Sarah: You're my home, Chuck. You always have been.
Sarah: Chuck, I want to spend the rest of my life with you. I don't care if you have the Intersect or not. Without you, I'm nobody; I'm nothing but a spy. Come back to me, Chuck. I want to marry you. (they kiss)
The final acts of "Chuck Versus the Balcony" are this, and seeing as this is kind of a Wham Episode, get ready to see a lot of white.
Where do we start? Ah, yes. Casey assuming the co-pilot's chair at Castle, helping manage Chuck's marriage proposal:
Casey: ...wait a minute...are you conducting a sub-mission? He's gonna pop the question to Walker, isn't he? Morgan: How did you know that? Casey: Because I'm a spy, not a moron. (sits down) You're right; he's gonna need all the help he can get.
Then there's Chuck's proposal speech:
Sarah: (glancing out at the Loire valley vineyards) I've been to so many places around the world, but I've never been to a place as beautiful as this. Chuck: I have. Every day. Every morning I wake up and I look at you, when we brush our teeth tandem-style, when we watch TV together, whatever, anything, always; every time I look at you, it's the most beautiful place I've ever been. (stuttering) I feel like I should be James Bond right now, you know? The guy who's standing on this balcony, with you right now in this moment, I mean— Sarah: I didn't fall in love with James Bond, I fell in love with you. (beat) Chuck: Sarah, I'm, I'm... I'm gonna ask you a question right now, so please don't freak out, okay? Sarah: I won't. Chuck: I want to spend the rest of my life with you. Going on missions, and saving the day, and being heroes, but mostly though, I just want to be with you. At your side. Always.
When that doesn't work out (they get interrupted), Casey offers this advice as consolation:
Casey: You know, I proposed once. (off Chuck's astonished stare) Kathleen. We had plans to go to Niagara Falls. I was about to ship out. We were young, and I was stupid, and things got screwed up, so I ended up proposing in a Buffalo bus station. Not exactly the most romantic spot in the world. But I'll always have that day. I'll always have that look on her face. Now the truth is, there's no such thing as a perfect moment, or a perfect spot. So: forget about the balcony, Bartowski. All you need is the girl.
The end of "Chuck Versus the Wedding Planner", Sarah's dad returns her piggy bank, stuffed with rolls of 100s, more than enough to pay for a dream wedding.
"Chuck Versus Agent X," in which Chuck and Ellie have their share of Milholland Relationship Moments, as between them Chuck reveals that he knows about Ellie working on the Orion laptop, and Ellie deduces that Chuck is still working with the CIA. Furthermore compounding this is the moment Chuck takes Ellie into Castle and shows him his Intersect capabilities.
Jeff's incredibly sweet and romantic video montage for Chuck and Sarah's rehearsal dinner in "Chuck Versus the Last Details". Given how disturbed Lester's version was and that Jeff has always shown himself to be by far the most odd of the two, it's a heartwarming moment for Jeff just as much as for Chuck and Sarah.
"Chuck Versus the Cliffhanger" has Chuck and Sarah's wedding scene, as well as the flashback in which they practice their vows. Also, when Chuck doubts that he'll be able to save Sarah without the Intersect, Casey stops that thought in its tracks, as no-nonsense and abrasive as he always has been but showing just how much he's come to respect and care about Chuck and Sarah:
Chuck: Casey, they took the Intersect out of me. Casey: Shut up. You're Chuck Bartowski, the second best spy I've ever worked with. Now you're gonna go save the best.
The wedding itself was absolutely fantastic. Chuck's vows (we get to see Sarah's ones earlier) and the little montage of their relationship going back to the first episode are everything the fandom could have hoped for. Check it out here.
Casey giving Morgan the Indiana Jones trilogy and telling him that there are only three movies, a key sign in noting that Casey had fully forgiven Morgan for his douchebaggery in the first few episodes.
In Chuck Versus the Hack Off, there's the final scene of Gertrude Verbanski making plans to break Casey out of prison. And getting some help from Morgan to get the big guy out of prison.
A blink-and-you'll miss it scene in the same episode has Chuck expertly shut off the baddie's security for their lair, allowing egress for Sarah and Gertrude. Sarah can't resist chirping "That's my man!", to Gertrude, with whom she had been debating the viability of spy & spy relationships.
Casey telling Alex to give Morgan another chance is pretty awww-worthy. Consider the fact that a few episodes ago, Casey really wanted to tear apart Morgan, so this particular scene from Chuck Versus the Santa Suit shows that the Colonel is willing to forgive and forget.
And after Casey gives it to her, Alex is seen happily holding the bear throughout the rest of the episode.
Pretty much the entire last third of Chuck Versus the Baby is one prolonged series of Heartwarming moments.
"Chuck Versus the Goodbye" might top them all.
Sarah has lost her memories of the past five years. At the end of the final episode, she sits on the same beach Chuck did way back in the first episode. She asks Chuck to tell her a story, Chuck responds by telling her the story of how they fell in love. He then tells her Morgan's theory that a kiss could bring back her memory.
(final words of the series)
Sarah:Chuck, kiss me.
In a meta-sense, the final scene - In the commentary track, Zachary Levi reveals that the direction he & Yvonne were given for the montage was "We need shots of you laughing & crying." They achieved this by talking about the past 5 years.
Also, before that, we see that all of his friends get happy endings of their own. Morgan and Alex moving in together, while Casey is off to search for Gertrude; Ellie and Awesome moving to their new job in Chicago; and Jeff & Lester seeming like they're finally gonna make it big in Germany.
The final interaction between Casey & Chuck? Casey happily hugs him, instead of accepting a handshake from Chuck. A stark contrast from the man who threatened Chuck when he hugged Casey at the end of season 2.
Casey: One things Russians do well — they give good hugs.
In the extended cut of the episode, Casey (Despite his protests a moment earlier) runs to Gertrude.