- "My Old Lady" was the first huge tearjerker for Scrubs. Three patients come in that J.D., Elliot and Turk all care for and J.D.'s narration in the episode mentions how "one in three patients always dies," foreshadowing that one of the three patients will die by the end of the episode. Instead, they all die. J.D.'s patient dies because she chooses to die because she's ready to die, Elliot's because there was simply nothing she could do to help in the long run and Turk's dies on the operating table during surgery.
- Doctor Cox looking at photos of him and Jordan in My Bad with a hint of fondness.
- Nick Murdoch completely breaking down at the end of the episode after being The Ace all episode because his patient (A seven year old) is doomed to die no matter what he does and completely quitting being a doctor because of it.
- Another minor one occurs in the episode "My Own Personal Jesus." Turk, completely joyous with Christmas spirit isn't letting any cynicism or criticism of his beliefs get to him. Cue montage of him trying to rest in the break room while on call during Christmas Eve only to be called out for emergencies each time all set to "The 12 Days of Christmas" with lyrics that get progressively sadder.
"On the twelfth day of Christmas my true love gave to me12 beaten children11 drive by shootings10 frozen homeless9 amputations8 burn victims7 strangled shoppers6 random knifings5 suicides4 beaten wives3 OD's2 shattered skullsand a drunk who drove into a tree"
- A minor one, but still sad nonetheless. In Season One, episode 15, during a psychology interview the main cast had to do, Doctor Cox winds up talking about his marriage with Jordan. He says that he kept trying to figure out why his friends who were married weren't trying to destroy each other like he and Jordan were. The words "They weren't unhappy. We were." really sold it due to Johnny C McGinley's acting ability.
- J.D. and Elliot's first attempt at a relationship. It goes from starting out well to crashing and burning incredibly fast.
- In "My Occurrence" when Jordan's brother Ben visits the hospital and at the end, JD finally admits that he was just hoping that he was wrong about Ben having leukemia.
J.D.: Ben you have leukemia.Ben: [Beat] Well that sucks.J.D.: [Beat] Yeah...
- Turk is concerned with the senior doctor's callousness and insensitivity to death, worrying that he's becoming just as callous. Dr. Cox then shows him a surgeon telling a family about how a patient recently died. He mentions that, unlike everyone else in the room, the surgeon is going right back to work. Dr. Cox tells him that making jokes and distancing themselves from dead patients is the only way for the doctors to manage daily. Dr. Cox's expression at the end is heart-wrenching.
- The end of the episode "My Philosophy" where the heart transplant patient dies and, in J.D's mind, goes out with a Broadway style musical, just like she wanted.
- My Sex Buddy's ending. J.D. and Elliot have been having casual sex all episode and J.D. realizes that he wants to have a real relationship with Elliot, who is unaware of this. She ends up breaking it off as J.D. wants to take care of her. J.D. expresses the heartbreak without her realizing it. The song choice sells it.
- In "His Story," the first episode narrated by someone other than J.D., we see a glimpse of Dr. Cox's life. He invites a large group of men over to his apartment to watch a football game. Later on, J.D shows up at his door to tell Dr. Cox that he plans to take a break from him for a while, which is brushed off by Cox who leaves J.D. to get back to the "big party" that's currently going on in his apartment. But after J.D. leaves, we see that Dr. Cox is all along in his apartment, with no one having shown up at all. It's the first real sign that Cox's jerkass tendencies might be entertaining once in a while, but they ultimately drive people away and make Cox a bitterly lonely person.
- This line from the ending of My T.C.W. - "Because nothing sucks more than feeling all alone, no matter how many people are around," - can sting just a little too much.
- Also from My T.C.W. - J.D.'s rant to Dr. Cox, Carla, Turk, and Elliot at the end before he storms out. Especially the last bit to Elliot:
And you! You know what, let's just - let's just forget for one second that a month ago you told me you couldn't be in a relationship with anyone. Because, for me, it's actually fun to watch you sabotage a relationship from the outside, it really is. Honestly, the only thing that gives me comfort, you guys, is while I'm sitting at home, staring at the ceiling, just wishing that I had someone to talk to, is knowing that none of you idiots realize how lucky you are!
- In "My Kingdom," Dr. Cox pulls a prank that makes everyone believe that Kelso has passed away. Instead of grieving, the denizens of Sacred Heart react to this lie with either indifference, pity for Heaven, or celebration. Kelso may not be a particularly good person, but the thought of literally nobody mourning your supposed death is harsh.
- "My Fifteen Seconds": After spending as little time as they can with Jill Tracy, J.D. and Cox realize that she tried to poison herself. The rush to the hospital and ask her how things have actually been going lately. The way she answers is particularly saddening.
Jill Tracy: Actually it has, uh, (choking up) been a couple of rough months.
- The episode "My Catalyst" has one of the show's most heartbreaking endings. When J.D. is about to confront him, he finds Dr. Kevin Casey obsessively washing his hands, revealing that his last surgery ended two hours ago but he can't bring himself to stop washing and go home. He is absolutely enraged at his body for failing him and himself for not being able to function properly, but tells J.D. that he isn't going to be someone who makes someone else shoulder their problems. The scene is immeasurably sadder by the fact that Michael J. Fox's Parkinson's Disease has all but forced him to retire from acting and is slowly destroying his body, but there is nothing that can be done about it.
Dr. Casey: Look, this isn't a strong moment for me... no one was supposed to see this.
- "My Screw-Up"'s ending, since it's revealed that Ben Sullivan was the patient that died earlier.
- There's a reason this episode won an award. How could it not when Cox actually CRIES in public
- Dr. Cox asking if Jordan's friends are still in town because he's wallowing in self pity and she needs someone to take care of her. Her reply: "I miss Ben." Simple and devastating.
- "My Brother, Where Art Thou?". JD tells his brother Dan he doesn't want to see him around anymore in some of the harshest language he can muster. Dan's response is fairly heartbreaking.
Dan: But I'm your brother. Doesn't that count for anything?JD: Not to me.
- The episode My Cake opens with J.D describing the different ways doctors break bad news to patients (the hand-on-shoulder, hand-on-hand, resident kabuki theater). J.D then states that his family has a different way of going about it, to which he opens the door to find his brother standing there with a cake.
Dan: ...Dad died.
- Hell, the entire episode can be both this and Heartwarming, especially when watching after the death of a loved one.
- The end of "My Last Chance", after Dr. Cox rants at the annoying, talkative paramedic he had to work with and asks what could've possibly happened in her life to make her that way. Denise breaks down and admits that the son she's gone on about is actually dead. Doubles as a Crowning Moment of Heartwarming when she mentions she thought the crew that tried to save him were amazing, and they inspired her to go into that line of work.
- The ending of "My Jiggly Ball". To explain, the episode revolves around J.D. being forced to write an introduction speech for Dr. Kelso at an awards banquet and desperately trying to find something good to say about him. Throughout the episode, Kelso is at his coldest, removing a terminally ill patient from a Drug trial in place of a rich patient who will make a donation to the hospital. Cox calls him on his callousness, asking him how he can not care about another person. Laverne notes Kelso's coldhearted attitude, saying that when he steps foot outside the hospital, he can be entirely happy despite people dying. The tearjerker comes at the end when J.D. notes that Kelso may be coldhearted but he would never want to have to make the same decisions he does. The final scene, where Kelso leaves the hospital and look of pure sadness and self-loathing crosses his face, is heartbreaking, made worse by the fact that he then quickly starts whistling happily as he passes by the gang, in order to maintain his Jerkass Fašade. The song ("Sideways" by Citizen Cope) and Ken Jenkin's brilliant acting absolutely sell it and show just how hard it is being The Spock.
- In "My Missed Perception", there's a patient who's in so much pain his wife mentions he couldn't even make it off the couch to go to the bathroom. It looks like Turk and Elliot are going to give up on him, until they catch the couple before they leave the hospital; and tell them that they're going to do everything they can to find out what's causing the pain. The looks on the patient and his wife's faces say it all.
- The end to "My Big Bird", in which the ghost/memory of Mr. Foster follows J.D., Turk, Carla, and Elliot through the hospital.
- The final moments of My Cabbage, where Cabbage accidentally infects Mrs. Wilkes after mishandling medical waste; the infection kills her in the following episode. The Coldplay song ("Fix You") playing in the background doesn't help the teariness.
- My Lunch, from start to finish. Three patients are all sick and need new organs. Jill Tracy also reappears and ends up in the hospital and J.D. thinks she died from a cocaine overdose because she was desperately lonely and J.D. ignored her when they ran into each other in public and blames himself. Dr Cox talks him out of feeling that blame and uses Jill's organs once she dies. It turns out she died of rabies and all three patients die.
Dr. Cox: He wasn't about to die, was he, Newbie? Could have waited another month for a kidney.
- Making it even more upsetting is that J.D. telling Cox that the patients would have died anyway almost works... right until the last one dies.
J.D.: Remember what you told me? The second you start blaming yourself for people's deaths... there's no coming back.Dr. Cox: *completely broken* Yeah... You're right.
- And then afterwards, a despondent Cox is storming out of the hospital. J.D. stops him and reminds him of some advice that Cox gave him earlier in the episode.
Dr. Cox: *looks at pager* Oh, God... come on...
- Even worse is Dr. Cox's reaction to his last patient dying. To see someone as typically level-headed as Dr. Cox completely flip his shit in impotent rage is... unsettling. Not to mention his reaction just before:
- Add to this the whole scene being framed perfectly with How To Save a Life playing just in case you didn't feel like you were being hit by a 2x4 yet. Scrubs always did frame scenes perfectly with music, but none better than this one.
- "My Fallen Idol" when Carla tells Dr. Cox that JD isn't coming. His reaction is slightly surprising; he's going to take a drink of his scotch but once Carla tells him the news about JD, he stops and seems sad. Considering how Cox treats JD most of the time, this is very moving and it shows you how much he cares about JD.
- JD's speech at the end, while heartwarming, was also incredibly sad.
- Carla's hysteria while she's in labour in My Best Friend's Baby's Baby and My Baby's Baby is mostly Played for Laughs, which makes it all the more upsetting when they take her to have a C-section and she sobs down the phone to Turk that she's really scared and needs him there.
- The whole episode of "My House" has us thinking that the woman next to Carla has post partum, but then the end of the episode cuts to Carla breaking down in tears while holding Izzy. It really hits home for those who have been through it themselves.
- The final song in "My Musical". Halfway through an upbeat, Grease-esque song, the patient of the week cuts in with a slow, sad melody reminding the characters (and audience) that she has a massive brain aneurysm, and she is terrified. The lines "What's going to happen? And will I be alive, tomorrow?" never fail to be heartbreaking.
- The ending of "My Cold Shower". After finding out Elliot's going to get engaged to Keith, every cast member has brief, absurd, comedic fantasies about how their married life with Elliot would be. Then when JD watches Elliot accept Keith's proposal, realises he's still in love with her, and we snap to a similar fantasy where it's just Elliot and JD sitting together on a couch, then to JD later crying in the shower.
JD: "You know what? I'm really happy that you're my wife."Elliot: "Me too."JD's inner monologue: As I looked at all the relationships around me: some that had gone on forever, some that were reigniting, and some that had just begun, I realized something...
- It's made even more striking if one notices that it's one of the few Imagine Spots where J.D. doesn't break eye contact or look to his left like he usually does. Instead, he's staring straight at Elliot the whole time.
- Once again, the music fits the scene perfectly and makes it that much more heartbreaking for JD, this time being Dashboard Confessional's Stolen
- The scene with Carla saying her parting words to Laverne in My Long Goodbye set to A Bad Dream by Keane.
- Made especially poignant considering that earlier Laverne was under fire from Cox about her beliefs in Jesus and how that her belief that everything was a part of God's plan kept her going when she had to see so many people injured, sick, and/or dying on a regular basis
- "My Dumb Luck". All of Dr. Kelso's scenes at that episode are touching, but the finale, as he resigns from his post, completely content, thanks Ted, with real emotion, for all his help over the years and finally drives off into the sunset with his picture on the back of his car is one of the most beautiful moments, managing to be a Heartwarming Moment, an Awesome Moment and a Tear Jerker.
- The ending of "My Princess". Dr Cox is telling his son Jack a fairy tale based on his day at the hospital, and ends it by telling him that the maiden, or patient, lived happily ever after. He then runs into Jordan who has been sat outside eagerly listening.
Jordan: So what happened to the girl? Did she make it?Cox: Let's just say that's the way I'm telling it.
- My Last Words. J.D. and Turk were going to go out for Steak Night, but they meet a patient named George who has no one to be with him in his last moments. They give it up to spend the night with George and try to comfort him. In the end, after all of their banter, they all admit to being afraid to die. The saddest part is his last words, after they smuggled him in a drink; "You know you guys... that beer... tasted great." The saddest part of that was the choice of music: "I Will Follow You Into The Dark" by Death Cab for Cutie.
- The end of "My ABC's" where JD explains that he's learned everything you need to know about life from Sesame Street and ends it with, "it's okay to cry sometimes" while he sheds a tear watching a mother console her 8-year-old son after his father has died from lung cancer after it had been in remission. A melancholy cover of "The Sesame Street Theme" by Joshua Radin is playing.
- Elliot having to tell a patient that they have HIV in My Full Moon and then telling Turk that if she could afford to not be a doctor, she would quit without hesitation because it can be so hard to have to diagnose patients with horrible diseases.
- My Finale: the montage scene where all the important people who have been on Scrubs in it's eight year run turn up to wish JD goodbye. It looks like a stereotypical series finale ending until the end when he turns around and we realize it's all in his fantasy.
- Where he's watching that film of events on the banner, culminating in Dr. Cox finally giving J.D. the hug he always wanted. Also, you can add in Dr. Cox's Engineered Public Confession that he actually respects J.D.
- The best thing about the Engineered Public Confession? When JD goes to hug Cox, not only does Cox not try to get out of it - if you look closely, you see that he actually leans into it. Not just the hug from Dr. Cox in the film, it's the JD getting as great a life as possible: he marries Elliot, has a child with her, stays close enough to spend Christmas with Turk and Dr. Cox, gets the fatherly hug from Dr. Cox, and JD's son marries Turk's daughter. Then, as JD's walking away he suggests that unlike the other fantasies, there's no reason why this one can't come true. It's an amazing sequence in and of itself, but add the fact that "The Book of Love" by Peter Gabriel is playing.