In "Mr. Monk Takes Manhattan", when Stottlemeyer confronts a New York police captain for concealing information essential to investigating Trudy's murder; specifically, he said "my friend's wife!" This was the first time Stottlemeyer ever called Monk his "friend," and for long-time watchers is one of the biggest "awwww" moments.
The episodes "Happy Birthday, Mr. Monk" and "Mr. Monk and the Dog".
Both of these just got blown out of the water by the Series Finale. Not only does Monk uncover the secret behind Trudy's murder, not only does he survive, but Randy gets promoted to police chief of Summit, New Jersey and moves there to be with Sharona. We also see Monk getting much better about his neurosis. Oh right...and his wife's daughter is totally fine, becomes a huge part of his life, and manages to make him extremely happy and even continue his work, despite having no reason to anymore, because other people out there need his help. Oh, and just in case you were looking for a moment from the other two major cast members, Natalie has a crying fit of joy because she can see Monk getting better (though not so much that she'd lose her job), and Stottlemeyer even gets a brief scene where he kisses his wife before heading out to solve yet-another case with his awesome friend Adrian Monk. This is all aside from the brief flashback sequence we have of all the best moments from the series, set to some very heartwarming music as things wrap up. So yeah...a fairly large departure from the downer ending people were expecting.
"Mr. Monk and the Kid"
Little two year old Tommy Graser finds a human finger, and is too young to understand the cops' request to show them where he found it. Monk, who think he's adorable, volunteers to take care of him. Naturally, he fails pretty hard, but the kid still adores him, and helps Monk solve the case. At the end, however, Monk tearfully admits that his OCD is just too severe for him to take on the many responsibilities a child requires, by reading the summation in the form of a bedtime story: "And even though Mr. Monk loved that little boy, he couldn't take care of him, because he can barely take care of himself."
In the Season 2 episode "Mr. Monk Goes to Mexico", Stottlemeyer gets a call saying Monk has died. He declares that if Monk doesn't get a police officer's funeral, even though he was technically no longer on duty, he would quit.
Captain Leland Stottlemeyer: I'm going to tell you something Randy, and I'm not ashamed to admit it. I loved that man.
Of course, the moment ends up being ruined when it is revealed that Monk is actually alive, and the guy who died was actually a lookalike, to which Stottlemeyer ends up saying, "I HATE THAT MAN!"
Also, during a barbecue held by Stottlemeyer (which was also the first one Monk ever attended since Trudy's death) in Mr. Monk and Mrs. Monk, he mentions that he thinks that Monk is the man in a rather heartwarming speech while focusing on the grill. Unfortunately, that one actually backfired due to the fact that Monk was away trying to get supplies, causing him to not only literally be talking to air, but Randy Disher misinterpreting the comment as being directed towards him.
In "Mr. Monk and the Genius," Stottlemeyer trying to convince Monk not to plant evidence.
Captain Leland Stottlemeyer: Don't do it.
Adrian Monk: Don't do what?
Captain Leland Stottlemeyer: Break my heart.
Pretty much any episode that ends with Monk fondly remembering Trudy with a happy smile. But one in particular always gets me right here, and it's not even a happy one. He has finally found Trudy's murderer. The man in question is on life support an dying he asks Monk to forgive him. In response Monk hits a switch, and as the man begins to gasp in agony, says, "This is me, turning off your morphine." Then he flicks it back on, and says, "and this is Trudy, turning it back on." Cue waterworks.
In "Mr. Monk Takes His Medicine," Monk is imagining Trudy as he longingly hugs her pillow to his face. He tells the imagined apparition that he can smell her lotion on the pillow, even after all these years.
Trudy: You never even liked that lotion.
Monk: (in tears) I love it now.
The episode that ended with him doing the fond remembrance of his therapist also does it. They had to write a new therapist into the show, as the actor playing Monk's therapist passed away and this was a really sweet way to honor his passing.
A smaller one, but one that not only warmed my heart but made me laugh: The end of Mr. Monk Goes to Group Therapy, when Harold Freaking Crenshaw says "Hey! My friend was talking!" and lets Adrian finish.
The entire scene with Molly on the beach in Mr. Monk and the End.
Another mild one from "Mr. Monk and the End": when Stottlemeyer tells the detectives that they won't be paid overtime for finding the guy who poisoned Monk, one of the officers replies "We're not doing this for the money."
Mild? That's a big moment, given that the men in the police department developed over the series to merely being amused by Monk's eccentricities and annoyed when he got in their way to respecting and appreciating him enough to do that for him. Not to mention when the one cop says he's not in it for the money, everyone else nods their assent.
Relatedly, Stottlemeyer and Natalie's reactions to finding out that Monk could very well die- even though they get frustrated by him on a regular basis, it's clear just how much they both love the man.
When Monk gets poisoned, and he needs to take a medicine to stay alive. He gets a pill given to try to relieve the symptoms, but there's no cure and he will die. He divides the pill into grains of medicine by color. Here this guy is supposed to be about to die, and here he is being very much himself.
Mr. Monk Meets His Dad. Monk and his father at the end with the bicycle.
A small one, when Stottlemeyer helps get Adrian out of a funk by calling in a favor and getting him a couple hours time in a clean-room lab setting where circuit boards are worked on. Adrian Monk, sitting in the cleanest surroundings one can get.
When Stottlemeyer gets married again, he asks Monk if he doesn't mind him marrying a woman named Trudy. Monk answers something like: "Of course not, everyone should have a Trudy in one's life".
The ending of Mr. Monk and the Magician. Monk and Natalie are watching Kevin Dorfman's video will (Kevin had been killed earlier in the episode), and it turns out that Kevin is rambling on in it in his characteristic way. Natalie asks him if she should fast-forward.
Monk: No. (smiles) Let it play.
in "Mr. Monk Meets the Playboy," Sharona tells her son he might be bullied at school soon because a bad guy owns some embarrassing photos of her. Benjy is obviously shocked, yet he tells his mom she shouldn't let a bad guy win just because he might have problems at school.
"Mr. Monk vs. the Cobra": Monk gets buried alive six feet underground. Earlier in the episode, an actual monk gave him a candle to bring light in dark places. He lights it, and soon loses himself in a hallucination of being with Trudy on what he called the happiest day of his life. Trudy tells him the candle is using up air and he should put it out, but Adrian doesn't want to because he doesn't want to lose any time he can have with her. When the police find him and dig him up, he's unconscious with a smile on his face and the candle still burning.
In "Mr. Monk and the Class Reunion," some of the flashbacks Monk has to his college years with Trudy.
In "Mr. Monk Takes a Punch," Monk figures out that boxer Ray Regis took a dive in the previous heavyweight title fight to pay for a series of experimental operations to save his trainer Louie Flynn's daughter Rebecca. But when Monk talks to Regis in private and informs him that he's aware of it, Monk reveals that he promises not to tell anyone else about this because he believes Regis and Louie had done the right thing. Regis is grateful enough to help Monk train in preparation for an upcoming fitness test.
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Mr. Monk Goes to the Firehouse
Mr. Monk Goes to Hawaii
When Monk and Natalie are in Natalie's hotel room and talking about her meeting with Dylan Swift. Monk explains the cold reader's M.O. and explains an incident they saw in a taping the previous day:
Natalie Teeger: That's not what happened with me, Mr. Monk. The first thing he said to me was that my husband missed me. He already knew stuff-
Adrian Monk: I'm sure he did. But think about what you gave him. A standard ploy a medium uses is to say your dead loved one has some unresolved issues to deal with, that he was cheated or wronged. Did he say that? [Natalie nods and sniffles] And what did you say?
Natalie Teeger:[as herself] "Mitch was killed two days before his twenty-seventh bithday. I'd say that was wrong." [as Dylan Swift] "It was an accident that took him from you." [as herself] "He was shot out of the sky by enemy fire! It was hardly an accident!"
[Natalie breaks down]
Natalie Teeger: Oh my God, I'm such a fool! [breaks down crying]
Adrian Monk:[takes her hand] No you're not. You just miss your husband very much. Tissue? [Natalie grabs a tissue from her purse and hands it to him] It's for you.
[Natalie blows her nose, puts it in a Ziploc bag, and puts it in the trash]
Natalie Teeger: Everything you're saying makes sense, Mr. Monk, except for one thing: you remember that bikini I was wearing? [Monk looks down at his feet as if she is wearing it right now]
Adrian Monk: Vaguely....
Natalie Teeger: I've had it for years. I bought it in Puerto Vallarta, where Mitch and I went to a weekend of romance, sun, and tequila, much to my parents' horror.
Adrian Monk: I don't need to know this.
Natalie Teeger: I lost my top making out in the water with Mitch. He had to get an emergency bikini from a beachside vendor while I stayed in the water. That was the one he picked out for me. After that, every time he saw me in that bikini, he'd remember how I lost the last one. He loved to see me in it.
Adrian Monk: I don't want to know this....
Natalie Teeger: Swift said that Mitch still loved my bikini. There's no way he could have known whether Mitch had ever seen me in it. For all Swift knew, I bought it last week.
Adrian Monk: You still want to believe in him.
Natalie Teeger: I want to understand how I was fooled.
Adrian Monk: These con men are very smart. They study up on fashion, songs, hairstyles, everything that is or was in vogue. He must have known the bathing suit was an older style, cut, or pattern and made a lucky guess.
Natalie Teeger: But what if he'd been wrong?
Adrian Monk: He'd have said, "What Mitch is saying is that he still thinks you're beautiful and will always love you."
Natalie Teeger:[tearing up] You'd better go, Mr. Monk, or I may cry all night.
Adrian Monk: That's okay. I don't mind as long as you've got plenty of tissue.
Monk getting past Natalie's indecency to treat a cut on her leg.
Monk telling a moving story to Natalie about Trudy's security blanket. It later turns out to have been a story he used as a trap to incriminate Dylan Swift.
Mr. Monk and the Blue Flu
Natalie describes the efforts of Monk's crew of eccentric detectives and their assistants to straighten up the squad room into a very orderly room. It brings tears to her eyes to see how much those guys respect Monk.
Mr. Monk and the Two Assistants
Mr. Monk In Outer Space
Mr. Monk Goes to Germany
Mr. Monk is Miserable
Natalie has mentioned that she honeymooned with Mitch in Paris. When Monk and Natalie are at the Arc d'Triomphe, Natalie suddenly, without any reason, breaks into a run. When she stops against an advertising column, she's practically in tears. Out of sensitivity, Monk is already giving her some privacy, leading to this particularly heartwarming moment:
Adrian Monk: Would you like a disinfectant wipe?
Natalie Teeger: No, thank you. There are some things a wipe can't cure.
Adrian Monk: I'm sorry.
Natalie Teeger: It's not your fault, Mr. Monk.
Adrian Monk: I know. It's Mitch. [Natalie is caught off guard by this comment]
Natalie Teeger: Then why did you apologize?
Adrian Monk: I'd forgotten until now what this place must mean to you. I suppose that it's changed since you were here with him.
Natalie Teeger: It's a stupid thing to cry about. Everything changes.
Adrian Monk: My life has changed a lot since Trudy was killed, and so has the world around me, but my feelings about her will always be the same.
Natalie Teeger: So what do you do about it?
Adrian Monk: I see things the same way I always have.
Natalie Teeger: But they aren't the same.
Adrian Monk: It's not what you see that's important. It's how you perceive it. Julie changes every day, but she will always be your little girl.
Mr. Monk and the Dirty Cop
When the summation is being given. Monk actually lets Natalie deliver parts of the summation. Her narration says, "Somehow he knew I was capable of solving this murder on m own and that was what he was making me do. He was guiding me the way a good, understanding teacher would with a promising student. It may have been the kindest, most sensitive thing he had ever done for me."
Natalie actually getting tearfully berated by Julie for almost getting herself shot in the final confrontation.