You can find a moment of heartwarming in Scrubs in My First Day. At the end, after J.D. realized what a terrible jerk Bob Kelso is, he is wondering "then who is the good guy?" just to get an emergency call and when he's trying to help the patient, he's surprised when Dr Cox actually gives him support instead of yelling at him. Dr Cox coaches J.D. through his fears of doing medical procedures on living patients instead of cadavers.
Mrs. Tanner comforting J.D. in "My Old Lady" after explaining him why she's ready to die.
Mrs. Tanner: Are you okay?
J.D.: I'm scared.
Mrs. Tanner: Come here. (J.D. sits on the bed and she hugs him) You're okay. You'll be just fine, don't worry...
At first, when Carla rants at Cox about her relationship problems with Turk, it seems like Cox doesn't care. Then he pranks Turk.
Cox: Nobody hurts Carla and gets away with it.
In "My Old Man", Cox shows up to listen to J.D. give his lecture on heart murmurs after J.D.'s father couldn't show up.
In "My 15 Minutes", Dr. Cox has JD write up his own evaluation. JD thinks he wasn't taking it seriously, but Cox rants at him that he wanted JD to really think about his abilities. However, when he's actually speaking to the board, he singles out JD and tells them that JD is hard-working, dedicated and very caring. It was a nice reminder that Dr. Cox really does have a high opinion of JD, even back then.
Dr Cox: I would like to make special recommendation of one intern. John Dorian. Smart kid, he's extremely competent and his determination to do better is something I see in him 24 hours a day. He cares. He cares too much. But he's someone you don't want to lose.
Elliot is having a hard time fitting in with anyone at the hospital. While things start to turn around at the end, there's two adorable scenes with Elliot and Laverne. The first has Laverne asking Elliot if everything is alright, and the second has her bringing Elliot a cup of hot cocoa because she's had such a rough time of it.
After requesting that someone other than Turk do his appendectomy, but then being rushed to surgery in the middle of the night while Turk is the only one on call, JD apologizes and tells Turk that he was an idiot and if he ever needs surgery again he wants Turk to do it. The fact that you can clearly hear the choked-back tears in JD's voice when he says so clinches the scene.
Which lends itself quite well to a Homoerotic Subtext-laden Brick Joke later, when it's mentioned that Turk's the only man that's ever been inside JD.
Doctor Kelso deliberately sabotaging the friendship that he and Carla were developing when he realizes that it's causing problems for her with the other nurses. Probably the first of many examples of Kelso keeping the hospital running by making everyone hate him.
In My Bed Banter & Beyond, all of the hospitals' employees are required to speak to a psychologist. When asked about relationships, Cox gives a jaded view , as do JD and Elliot, whose recent relationship is shown to be falling apart. However, Carla and and Turk talk about how happy they are with each other and admit that they love each other. It showed that relationships can work and always made this troper a little misty.
Ben overall is pretty amazing in My Hero. The guy is not exactly a saint, but after he was announced to have acquired leukemia he suddenly vanished. Soon after they find Ben in the children's ward playing with a bunch of laughing, giggling children. You gotta admit, that's really just so sweet of him.
Doctor Cox dealing with his fear that Ben might die and being there for him anyway.
In the Season Finale, Doctor Cox willingly agreeing to help JD with a patient with no insurance because JD's strong sense of compassion is why he took on JD as a protege and why he trusts him as a doctor and person.
When Dr Cox takes a heavily pregnant Jordan back and she nearly goes into a premature labor, Dr Cox is immediately there the first chance he gets and openly shows a lot of concern for.
During My Sex Buddy, Elliot is just so frazzled and unable to do her job properly after being cut off financially by her dad and then evicted from her apartment that he paid for. While staying with J.D. and Turk, she's sleeping with J.D. the whole time and it's not helping her at all. Turk tries to help by getting all of her patients to ask for a new doctor so Elliot has time to get her life on track and Dr. Cox ends up having to talk to Elliot and say that it's not easy to balance your personal and professional life, but it's doable and to get her life in order. He then says not to tell anyone.
Dr Cox trying to care for Jordan when she's about to give birth, then getting J.D. to keep an eye on Jordan for him and then bursting into Jordan's room and refusing to leave in My Karma.
Dr Cox: Hey, Girl's Name!
Dr Cox: Give me a break, I've got a lot on my mind, Ellen. Oh look at that, I bounced back! Anyway, the cavebat just kicked me out of it's lair. So I need you to go in there and occasionally poke her with a broomstick and see how she's doing.
J.D.: Dr Cox, I-
Dr Cox: A but but but! Please, just check on her.
In the next episode, Dr Cox mentions to J.D. that he's trying his hardest to make his relationship with Jordan work this time and hopes that he's doing the right thing.
Another Dr. Cox one, in the season 2 episode, My Interpretation, he is trying to not spend time with Jordan's son (He's unaware that it's his at this point). Partially because of annoyance and partially because when when Cox looks at him, he doesn't feel anything. So one day he goes home to tell Jordan this when she's trying to give her son a name. After a second he suggests, "Jack?" in a not so serious way. In response, the child giggles and smiles, and so Jordan says that he'll be named Jack while Dr. Cox stares at him, his expression surprised as he realizes that he does care for the boy.
The Dr Cox and Jordan subplot of the second season finale, when Cox finds out that Jordan's baby is his, Cox makes it clear that whilst he's mad at Jordan, he wants to be part of his son's life and tries to break up with Jordan, who refuses to do so since Jordan refuses to play their game of "One person walks alway and the other is too stubborn to go after them" and refuses to leave him alone until he agrees to come home with her. He finally caves in and agrees.
When Cox is confiding in J.D that he's scared that he'll be a terrible father to Jack, J.D. points out that Cox will be a great father, since he sent J.D. and Turk home for drinking whilst on call and they deserved it. Cox and J.D. sees Kelso picking on Elliot to make her cry, J.D. outright says that if Cox was Elliot's dad, he'd know what to do. Cox punches Kelso in the face and outright tells Elliot that she's doing a good job before he leaves with a big grin on his face. Just Watch It.
Dr. Cox punches Kelso in the face
Dr. Cox: You're doing fine Barbie.
Elliot: Thank you?
Dr. Cox: Everyone have a good one! I'm going home to see my son.
The ending for My Brother, Where Art Thou. Dan secretly confronts Dr Cox about being J.D.'s mentor and demands he takes it more seriously, or he would have to answer to Dan.
Dan: Listen, Dr Cox. No offense, I'm a big fan of the tough guy act, but let me tell you want I really think. I think that you love that these kids idolize you, Johnny does. Johnny was the one we all knew was going someplace, sweet kid, smart kid. Becoming a doctor, this is all he ever wanted, but somehow, you found a way to beat that out of him, haven't you and turned him into some cynical guy who seems to despise what he does. Dr Cox, Johnny's never going to look up to me, ever. But he hangs on your every word. So I'm asking-I'm telling you, take that responsibility seriously, stop being such a hardass or otherwise, you're going to have to answer to me.
In My Screw Up, after Cox's rant to JD about the birthday party, the sudden return to reality at the end and the line "Where do you think we are?". Cox shows genuine emotion and sadness as Jordan and JD comfort him.
In the subplot, Kelso has been dodging Carla, who's seeking advice about Turk's mole, which she hates. Kelso relates to her a story about Enid's snoring and delivers the Aesop that the thing she hates so much may be what she misses when it's gone.
Very minor one, but when they are at the service, JD is in the front row, a place for family and close friends. It shows that JD was relatively close to Ben and Dr. Cox.
In another episode, Kelso goes to great lengths to treat his gardener. Carla points out that this gardener has known Kelso for years, and doesn't seem to hate him. Cox inquires if Kelso is secretly a good person off the clock, and though Kelso tells Cox it's none of his damn business, we later see Kelso treating the gardener's whole family to ice cream.
In My Clean Break, the framing device of the episode is that Cox is talking to his therapist about how he's happy with his family and it's affecting (negatively) his abilities as a teacher, and the realization that he's only effective as a teacher when his pupils fear him, then closes it out saying "I'm telling you this because it's going to affect you", with the reveal that he's been talking to his infant son.
It's always great when J.D and Turk have a heart-to-heart. In particular, My New Game's ending, after J.D. briefly doubts Turk after a patient dies whilst he's operating on the patient.
JD: Dude, it was one second of doubt. Since when do you care what anyone thinks?
Turk: I don't, I care what you think.
The 4th season Christmas episode, My Best Moment. J.D. promises a patient who comes in with a son that he'll be home by Christmas, only to be immediately reprimanded for making such a hard-to-keep promise. Not only does the patient survive, but the episode ends with the main cast reminiscing over how great that moment was.
In "My Cake", Dr.Cox spends the entire episode trying to help J.D by taking all his patients, trying to offer him a hug and then in the end, rallies Dan, who'd been sitting in the bathtub the entire episode. To comfort him in a way that everyone involved is comfortable with, Dr.Cox and Dan sit with J.D drinking beer, talking about his father and Dr.Cox and Dan admitting they are proud of J.D.
After JD's dad dies the janitor steps aside to let him get in the door and doesn't hassle him all episode.
"In loving memory of our friend John Ritter" sold it for many as well.
In the subplot, Turk finds out he has type two Diabetes and takes the whole episode to admit to Carla that he has it, but instead of yelling at him for not telling her straight away, she's completely supportive and already knows and has sugar free food recipes and articles for him.
In My Best Laid Plans the Janitor's little moment with Elliot is pretty heartwarming.
Janitor: You're the only one around here that treats me like a real person.
Elliot: What did you say?
Janitor: There was one other girl a few years ago, red haired doctor. She used to eat lunch with me until the other residents made fun of her. They called her "Janitor lunch eater", not the most clever group. Anyway, I know that you don't think about me the way I think about you and I never really believed that you would or that you could. But just pretending for today made me feel good for a change. I'm sorry.
Elliot: You know what, it's ok. I actually had a good time.
At the end of My Jiggly Ball, when, after a patient dies because of him, Dr. Kelso steps out of the hospital, and, instead of whistling carefree like he always does, is still obviously troubled, showing he does care. Especially when the main cast walks by and he tries to resume whistling to hide the fact.
Dr.Cox showing up at his son's baptism, even though he hates that it's happening. Followed by explaining to his sister why he hates seeing her (He can't stop thinking of his Dark and Troubled Past when he sees her and she admits it's hard for her too) and making the effort to not let it stop her from being there for his son's birthday and having a quick game of Basketball before she leaves to head home.
J.D. giving Keith an interesting medical case not out favoritism, but because he's genuinely the best intern, at the same time admitting to Elliot and himself that he's a good guy.
J.D. and Cox finally getting over their grief about Mrs. Wilk's death in "My Five Stages".
When everyone is hugging after Carla announces her pregnancy (to Kutless's 'All Of The Words', no less) in Scrubs, you can't help but feel all warm and fuzzy inside.
Following the scene right before when J.D. narrates, "Then I witnessed one of those moments that let me know in my heart that these two would be together forever."
Another great one is the end of the Janitor's viewpoint story in His Story III. A patient who was mute could only speak through a program that allowed him to type through a series of blinks on his computer. After it breaks, the Janitor makes repeated visits to the patient to talk to him all day long and keep him company. When the new computer finally arrives, the patient thanks the Janitor for being with him.
Especially how the sequence is presented. For most of the episode, it looks like the Janitor is just bothering this patient who just continues to look at him with this blank, bewildered expression on his face. Only at the end do we learn that the patient can't talk and requires a computer to help him speak. What's especially heartwarming is (a) the notion that the Janitor spent the day with him and keep him company, talking to him like a real person and not like just information on a chart and (b) the Janitor doesn't hear the patient's "Thank You," but he continues on nonetheless. The Janitor does make a difference in people's lives, in his own way.
In My Fallen Idol, J.D. tells Dr. Cox that, even though he gave three patients that could've waited a little longer transplant organs filled with rabies, he made the right choice and that he's proud of him. "Not for doing your best, but, after twenty years of being a doctor you can still take it this hard." The whole scenario lets you know both that everybody likes Dr. Cox and he actually does care about J.D., actually calling him by name to thank him. Tears abound.
Jordan helping Carla through her postpartum depression.
The Guy Love song.
Dr. Cox is sitting in the doctors' lounge watching TV, running over in his head all the negative, lifelong implications of the fact that prenatal surgeons are working on his and Jordan's second child. He's thoroughly worried and upset... and all that goes away when he learns he's going to have a daughter.
Jordan telling Dr. Cox that she's really glad she has him in her life after he's been working hard to take care of her after some surgery she had to have earlier in the season.
Kelso hadn't been speaking to Elliot after she went to private practice. But when she wound up with a deceased patient's dog, she entrusted it to Kelso, who's own beloved Baxter had recently died. Kelso lifts Elliot's suspension for bringing the dog to the hospital in the first place, though he does remind Eliot that he thinks she's a miserable excuse for a doctor, keeping up his normal facade.
The entire episode when Laverne dies., also a Tear Jerker.
The ending of my labor 'My Hard Labor'.
The end of the episode 'My Dumb Luck'. Especially Kelso's last line on screen and 'Ted, thanks for everything. Sincerely'. This doubles as a Tear Jerker.
Hell, that whole damn episode. Kelso's scenes with Boone, especially telling Boone he's gonna love his next 20 years at Sacred Heart, him thanking Elliot and Carla, and when Boone says that Kelso really does love SH.
J.D. and Dr Cox talking like equals in the cafeteria. J.D. ditched his interns and Cox is finding out why and after listening to J.D. vent how he's tired of the interns attitudes and ignorance and just plain tired, he's sympathetic and understands how he feels, since he's tired of having to be the thankless Morality Chain for the Chief of Medicine that he was for Kelso. Cox also mentions having an intern who pissed him off so much, his therapist put him on a suicide / homicide watch. That intern became a pretty good doctor though.
J.D.: So this intern you mentioned earlier, I bet he turned out to be a pretty amazing doctor, huh?
In My Last Words, Turk and JD give up their "Steak Night" to spend a night (and a beer) with a dying patient. Their last conversation, and George's death is set to "I Will Follow You Into the Dark". After George dies, they go to the roof and fire a flare gun into the night. "Goodbye George"
JD's "Mr Longbeard Stinkypants" story from same episode showing the quiet level of impact his father was able to have in a random homeless man's life through simple kindness.
At the end of "My Happy Place" when JD and Elliot get back together after Kelso tells them to "screw what everyone else thinks and do what makes you happy". It's a double-whammy because JD and Elliot get back together and Kelso sits down and admits he loves his life at Coffeebucks.
After Kelso's retirement, he and Dr. Cox finally bury the hatchet when Cox asks him to help remove the new Chief of Medicine, who is even more of a Jerkass than Kelso was. Kelso agrees, but only if Cox will admit to having missed him. Cox states that while he always hated Kelso, he did feel that his former foe had managed to look the other way a couple of times while Cox was bending, stretching or breaking rules, and that Cox felt that he (Kelso) was burdened by the job he had to do.
After Ted suffer's a severe shock from seeing Kelso back in his old office, Kelso puts a blanket on Ted and asks J.D. if everyone is still taking care of him since he left.
This also doubles as a Crowning Moment of Funny when JD explains that they've been taking Ted on walks and then Kelso scratches Ted behind the ears.
After Cox is promoted to the Chief of Medicine position (On Kelso's recommendation), Kelso explains that it is now up to J.D. to keep Cox focused on what's important, because he's out of his element, and that J.D. must now fill the roll that Cox filled when Kelso was Chief of Medicine.
Ted, the hospital lawyer and the girl he has a crush on doing a duet in the episode "My Lawyer's in Love." D'awww.
Turk asks new intern Howie (a shy, bespectacled type) how he got a difficult patient to take his medicine.
Howie: I may have given him a little slap
Turk: You'll do fine here.
Don't forget the ending of "My Soul on Fire Part 2". Janitor's wedding to Lady, itself a crowning moment of heartwarming, inspires a collection of crowning moments of heartwarming for each major couple to Ted's acoustic cover of "Hey Ya", which makes everything seem more poignant and beautiful (and wacky at the same time too, in classic Scrubs fashion). From Carla putting aside her mommish ways for the moment to be the sexy mate Turk had missed, to Jordan bringing herself closer to an healthy relationship with Cox by admitting genuine affection for him (accompanied by Cox's reaction of grabbing her and jumping into the pool with her) to the king of crowning moments of heartwarming between JD and Elliot, when he gives her the tiki amulet after delivering possibly the most heartwarming and romantic confession in the entire series:
JD: I never really believed that I'd find somebody that I'd love as much as you. I love you more than anyone in the world. Elliot... I love you more than Turk.
My Finale is full of these, especially when JD made his good-byes to everyone.
The JD/Carla scene was wonderful:
Carla: Tell me my husband loves me more than he loves you.
JD: It's about the same.
Carla: I'll take it. I'm gonna miss you Bambi.
JD: I'm gonna miss you too.
One that doubles as a Crowning Moment of Funny: JD gives Dr. Cox a present: a book of all the long-winded rants Cox has ever made to JD. The two of them read the one from "My Old Friend's New Friend" together.
J.D. saying goodbye to Elliot and Turk by telling Elliot that yes, he wants her to move in with him and if he didn't, he'd make it obvious and telling Turk that his goodbye was perfect.
Jordan legitimately giving JD a heartfelt goodbye, simply because it was so out of character. Her reasoning, being she wants to be nicer to people "For my stupid kids" should count
Right after that, Ted allowing Jordan to be horrible to him, because it "seems like you need it". Also notable that Jordan visibly struggles to come up with something mean to say about him, showing she's finally softening up
J.D. and the Janitor parting on good terms, not to mention J.D. finally learning the Janitor's name. It's Glenn Matthews.
Dr Cox's speech to Sunny.
Sunny: He's finally gone. Talk about making a big deal over nothing, y'know? I mean, Dr Dorian was fine, but he was no better than any other doctor.
Dr Cox: For the record, he was the best that ever came through this dump. John Dorian was the first and only doctor I ever met who cared as much as I do, and you can forget about him being just an exceptional physician. 'Cause the fact of the matter is, he's a damn exceptional person. That's why people gravitated to him. That's why I did. He was my friend.
Of course, Dr. Cox's reaction when he realizes that J.D. heard (and in fact planned) the whole thing doubles as a Crowning Moment of Funny.
ESPECIALLY the ending where he walks down the hallway to the front door, where all the Scrubs characters throughout the years send him off. Out the front door, he looks on at his "Goodbye JD" tarp and imagines his future with a pregnant Elliot, his friendship with Turk, and finally getting his hug from Dr. Cox. All ending with the creator Bill Lawrence himself playing a janitor who takes down the tarp. He bid JD a good night; and JD thinks to himself, "Who's to say my fantasy won't come true, just this once?", implying that the future JD imagined for himself WILL happen. And finally, JD drives away from Sacred Heart Hospital, ending his last day there all the while a slow instrumental to the Scrubs theme playing.
The Janitor quit Sacred Heart the day after the Season 8 finale, purely because he realized JD wasn't coming back & had genuinely left the hospital.
The whole arc with Cole wanting to become a surgeon, simply because Turk had saved his life and he wanted to do the same for others. As maligned as Season 9 was, this was a genuine good moment for the character.