- The climax of "Sucker Punch", and the sight of Beckett desperately trying to revive her mother's killer.
- In last five minutes of the season two finale Beckett realizes that she's in love with Castle, dumps Schlemming, and tries to tell Castle that she loves him, only to be interrupted by his ex-wife/publisher/Romantic False Lead, with whom he's going to the Hamptons for the summer — with everyone watching.
- Beckett has a private sad face after finding out that her former training officer is a criminal. To get a trace on his phone, she also has to confess some of her private thoughts to him while everyone else is listening. To avoid a total break down, she then has to say that it was all an act.
- Martha's reaction to Chet's death makes you feel for a character that never even appeared on screen.
- In "Setup", Castle sending Alexis to the spa with her grandmother to get her out of the city in case the dirty bomb they're trying to find goes off. Just the look on Castle's face when Alexis looks away and the fake smile that doesn't quite reach his eyes...
- "Setup" and "Countdown" give us Agent Fallon, whose wife was in the Towers on 9/11. He was on the phone with her when she died. Then at the end of "Countdown", he's on the phone with Castle and Beckett, unable to help them defuse a bomb.
- "Knockdown" definitely had its moments.
- One in particular is after Castle and Beckett are shot at by a sniper, Martha expresses her concern for Castle's safety. When Castle asks her where this is "coming from", Martha tearfully and angrily replies, "How the hell can you ask me something like that? Think about how much you love Alexis and that is how much I love you. So don't you dare ask me where this is 'coming from'!"
- "Knockout", the season 3 finale. Captain Montgomery's Dying Moment of Awesome, the Cliffhanger, Montgomery was betraying them all, Kate gets shot.
Castle: Ssh, Kate. Stay with me, Kate. Don’t leave me, please. Stay with me, okay? Kate, I love you. I love you Kate.
- Two moments in particular: During his talk with Hal Lockwood there is a moment when Montgomery closes his eyes. Given the context of his speech to Kate and that Lockwood is giving him a choice between his family or Beckett, you know this is the moment he realised his only option was to die. And right near the end of the episode, we see that Castle is one of Montgomery's pallbearers. It's a tiny moment given no pomp, but it truly highlights the importance of Castle within the precinct at this point.
- The end of "When The Bough Breaks".
This was my family. We were happy once. Now they're gone from me. Both of them. Gone.
- The interrogation of the victim's former husband rapidly turns into this as soon as he learns she's dead. He's clearly heartbroken when he learns this, and then he explains what tore them apart — their young son, slowly dying of an incurable disease.
- During "Kill Shot" when Beckett's worsening PTSD is keeping her from working the case, Esposito takes her into the back room to show her the rifle that shot her and talks her through what helped him.
Esposito: I've been where you are, I know what you're going through....You're not fine, you're just trying to act like you are. This is just a tool; it's a hunk of steel. It has no magical powers and the person that fired it is not some all-powerful god. It's just a guy with a gun. Just like the guy we're hunting now, and like every other bad guy, he's damaged goods.Beckett So am I.Esposito That's right, and that's ok. You think it's a weakness? Make it a strength. It's a part of you, so use it.
- The part in "47 Seconds" where Castle, arriving late to the station and hearing Beckett interrogate a suspect, hears her say something that makes him realize she remembers him saying he loved her after she was shot and has kept him in the dark about it for the whole year. The look on his face is so heartbroken.
- The look on Beckett's face in "The Limey" when she asks Castle if he's feeling okay - which is her unsure attempt at trying to ask him why he's been so distant the past few days, since she does not know he knows the truth about her trauma - and he says, "Never better" before heading towards the Body of the Week. She really has no idea how to get through to him and it's heartbreaking.
- The episode "Always" has a large one when Castle reveals his secret deal to keep information from Beckett to save her life, while finally admitting his love for her. He can't stand to see her risk her life and makes the decision to walk away when she chooses her case over him. Also on Beckett's side when, despite her bravado about the case and anger towards him, she's clearly heartbroken and holding back tears when he actually does turn and walk away from her.
Beckett: Listen to you?! Why should I listen to you? How am I supposed to trust anything you say?!
- When Beckett learns Castle's secret that he's been keeping throughout the season that he has contact with the man who is keeping blackmail material on her mother's murderer as leverage for her protection, she's understandably angry and hurt at the betrayal and lashes out, demanding to know how she can even trust him any more after this:
Castle: [gut-punched] How are you... ?! Because of everything we've been through together! Four years! Four years, I've been right here! Four years, just waiting for you to open your eyes, to see than I'm right here! [Near tears] And I am more than a partner! Every morning I-I bring you a cup of coffee just so I can see a smile on your face, because I think you are the most remarkable, maddening, challenging, frustrating person I have ever met. And I love you, Kate. And if that means anything to you, if you care about me at all, just don't do this.
- Beckett's resigning after failing to catch the man who shot her. Equally as tear jerking is a following scene when it turns out she doesn't care about catching him anymore, and simply wants Castle.
- "Probable Cause" gives us Beckett in pieces when evidence implicating Castle as the murderer keeps mounting, and that according to her, Castle's behaviour once he was locked in a holding cell and shown the undeniable evidence implicating him while the DA filed charges against him were that of a "lost little boy".
- Meredith's explanation of why she left Castle is actually pretty sad. Well, ignoring the fact that she also cheated on him, which she conveniently fails to mention to Beckett.
- Kate's explanation in "Secret Santa" about why she takes the Christmas Eve's night shift every year: her mother died on January 9th, and they had yet to pull down the Christmas ornaments, so when they did, they felt as if Christmas had died for them, so they never opened the ornaments' boxes again and they never celebrated it again.
- The last ten minutes of "Kill the Ballistics" has a notable one from someone not from the main cast: The victim of the week is a girl named Jane, who was in a relationship with a boy named Ben whose family has ties with the Triads. Ben and Jane planned on running away together, but once his brother Phillip found out the plan, he killed her. When Ben approaches his brother to confirm what's happened (and to get a confession so Beckett and the others can arrest him), Ben breaks down - partly because his brother keeps dodging his questions (and thus not getting enough of a confession needed to charge him), but also largely because he can't bear the thought of his girlfriend having died in such a brutal manner. The actor's delivery in the scene what really sells it:
Ben: Philip, if they hadn't found Jane - if she'd stayed hidden - I mighta never known what happened to her. Would you really have let me wonder for the rest of my life? ... So I could pretend she was alive somewhere like a child? SHE'S NOT MISSING!! She's dead, and I'm not a child!! I-I have to know, did she cry - di-did she ask for me?! I need to know!!
- The subsequent police raid that interrupts the brothers' conversation is heartbreaking as well - Philip is tackled to the ground screaming at his brother for being a rat. Ben pulls a gun out to point at the police when someone in the squad shoots him square in the chest. Ryan, who's spent this entire episode trying to make up for the fact the victim of the week was killed with his (stolen) firearm, drops everything and tries his best to resuscitate Ben and whispering 'I'm sorry' over and over to himself and to Ben - while Philip screams turn to despair at his brother's death. Turns out, it was a ploy to get Ben away from his family and into witness protection - but it doesn't make the moment any less emotional.
- Castle's break-down when the van that took Alexis and her friend, Sarah (the intended target), was found with a large pool of blood and the large implication that it could be Alexis'. Thankfully, it isn't her blood (nor Sarah's), but the poor guy is suffering enough with the fact that Alexis was kidnapped in the first place!
- In "Still", Beckett cries as she remembers everything she has done with Castle as the bomb countdown is about to end.
- In "Dreamworld", Castle is poisoned with a toxin that will kill him within a day. The feds allow him to help with the case but refuse to let him leave the building with Beckett. The two share a look. Though nothing is said, they both know that this might be the last time they see each other.
- The doozie dropped at the very end of "Need to Know", when Beckett is fired for doing the morally right thing, immediately after Castle had shown her the key to their new DC home... The Mood Whiplash in that scene is just devastating.
- Despite having an over all hilarious episode, "Time Will Tell" has one heckuva Bittersweet Ending: Alexis is moving out, to move in with Pi, and Castle just can't wrap his head around the fact that his little girl has moved onto that stage in her life.
(Alexis leaves, having said her goodbyes.)Castle: Too soon.
- "Time Will Tell"'s ending is nothing compared to "Get a Clue"'s. Castle asks Alexis if they can go for some make-up ice cream. And for the first time ever, his daughter tells him no. Gah. My heart.
- The entire second half of "Under Fire", full stop, particularly Ryan calling Jenny from the sub-basement of the burning building he and Esposito are trapped in to tell her goodbye and the two of them finally deciding on names for their baby and choosing Javier if it's a boy.
- The ending of "For Better or For Worse". After an entire episode where Castle and Beckett's wedding falls apart little by little, with them picking up the pieces, it looks like they will finally marry. Then Castle gets followed by a mysterious car. The last shot of the episode is Beckett crying at the sight of Castle's car on fire.