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Dean's talking with Lucas in "Dead In The Water", even though the boy is mute. You can tell that he feels similarly, as both of them have lost a parent and still haven't fully come to terms.
In "Skin", when Sam admits he's never fit in at Stanford, Dean calls him a freak. And then he says this. "I'm a freak too. I'm right there with you, all the way."
The land developer in "Bugs" saying "This has been the biggest financial disaster of my career, but somehow, I really don't care" and smiling as he looks over at his son. Seeing them reconcile makes Sam want to apologize to his dad when they find him; this is really the first turning point in Sam's view of John.
The end of "Nightmare". Dean telling Sam "As long as I'm around, nothing bad is gonna happen to you"...
John's reunion with his boys in "Shadow" before the daevas attack and Dean convinces him to leave again because he knows that he and Sam will only be used against their dad if he stays with them. You've got Dean striding over to his daddy and hugging him with no embarrassment and then Sam (the disowned one, remember?) doing the same.
There's actually a moment's pause when Dean lets go of John, and John looks over at Sam. There's a look on Dean's face that's a mix between hope and terror, like he's wondering whether the two are going to strangle each other or reconcile. Sam looks unsure - he wants to make up with his dad, but his relationship with his dad has been rocky at best. And then John smiles, and the two hug.
This from "Dead Man's Blood":
John: I don't think I ever told you this but... the day you were born, you know what I did?
John: I put a hundred dollars into a savings account for you. I did the same thing for your brother. It was a college fund. And every month I'd put in another hundred until... anyway, my point is, Sam, that this is never the life that I wanted for you.
Sam: Then why'd you get so mad when I left?
John: You gotta understand something. After your mother passed, all I saw was evil, everywhere. And all I cared about was keeping you boys alive. I wanted you... prepared. Ready. Except somewhere along the line I... uh... I stopped being your father and I... I became your drill sergeant. So when you said that you wanted to go away to school, all I could think about, my only thought was, that you were gonna be alone. Vulnerable. Sammy, it just... it never occurred to me what you wanted. I just couldn't accept the fact that you and me? We're just different.
John:(smiling a little) What?
Sam:We're not different. Not anymore. With what happened to Mom and Jess... well, we probably have a lot more in common than just about anyone.
John: I guess you're right, son.
Sam: Hey, Dad? Whatever happened to that college fund?
John: ... I spent it on ammo.
[Sam and John look at each other and start laughing.]
He might have screwed it up all again five minutes later, but John finally telling Dean that he's proud of him in "My Time Of Dying" and also pleading with Sam for them not to fight for once.
The man in "Crossroad Blues" who knows the demon is coming for him and gets his wife to leave the house, simply telling her he'll love her forever. Later you find out that his deal was to save her from cancer.
"Croatoan" has Dean defending Sam, who is supposedly infected with the Croatoan virus, from the rest of the uninfected and later staying with him rather than go off with the survivors and let Sam kill himself (although that one's slightly more disturbing than the other).
The Sarge: Look, I understand he's your brother, and I'm sorry, I am. But we gotta take care of this. (pulls out his gun)
Dean: I'm gonna say this one time, you make a move on him, you'll be dead before you hit the ground, you understand me? Do I make myself clear?!
An extremely creepy example, but at the end of 'Playthings', after the Grandmother [[spoilers: sacrificing herself to her dead sister, who has been acting as her Granddaughters muderous imaginary friend]], seeing the two finally reunited in death, skipping in one of the hotel rooms and both look really happy.
While most of their heartwarming moments have disturbing or depressing undercurrents and while some are shown to be flat-out lies by later episodes, Sam's "You're my big brother. There's nothing I wouldn't do for you" in the finale is certain to make any troper's heart melt a little.
Dean walks into the cabin and sees Sam alive again. He swoops over and pulls him into a crushingly tight (albeit one-sided) "I'm really glad you're not dead anymore" hug.
There was a moment in "A Very Supernatural Christmas" when Wee!Sam realised what an utter bastard his father was and acknowledged that Dean was the real caregiver, his real father figure, and the most important person in his life. And how did he show it? By giving Dean the amulet that he even wears when he gets dragged down to hell.
Not only that scene, but the ending scene where Sam and Dean open each other's ordinary, but thoughtful, gifts was incredibly heartwarming.
There is also one line when Dean reveals to Sam what their father actually does. Sam is understandably terrified, and says something among the like of "But Daddy said the monsters under the bed weren't real." Dean's response? "That's because he already checked there." Something about that is just amazingly daw-inducing.
The two brothers singing together in "No Rest for the Wicked."
Also from "No Rest for the Wicked." Bobby catches the brothers trying to sneak off saying it's not his fight. Bobby's response? "The Hell it isn't! Family don't end with blood, boy!"
The amulet gets a double whammy in "Lazarus Rising". The first one is realizing Sam wore it under his shirt in the four months Dean was gone and the second one is him giving it back to Dean, who looks just as touched as he looked when he first got it.
Dean's shirt and jacket swap—Dean is wearing Sam's clothes! That's so sweet!
The mutual hug was also adorable. You could really tell how much they cared about each other.
Dean's reunion with his beloved car was also heartwarming. "Did you miss me, sweetheart?" Oh, Dean, you have no idea.
When Bobby finally realizes that Dean is really Dean, you get another tight hug.
There was a "blink-and-you'll-miss-it" moment in "Are You There, God? It's Me, Dean Winchester". Dean nearly gets his heart ripped out by the ghost of Henriksen, Sam shoots it with rock salt, Dean falls to the floor, Sam asks him if he's okay and the obvious answer is no. And now for the sweet bit: Jared Padalecki's massive hands clasp over Jensen Ackles's relatively tiny hand and pulls him up. In a season where the brotherly love has been so strained lately, you take what you can get.
In "In The Beginning", when Dean realises that he didn't change anything and watches Young Mary hug John who almost died, Castiel arrives and lays a hand on Dean's shoulder, looking at him compassionately.
Earlier in the episode is a minor one when Dean finds out who he and Sam are named after: Grandpa Samuel and Grandma Deanna.
Threats of violence can be heartwarming, too! In "After School Special", teenage!Dean finds out that a boy at their new school had beat up Sam, and responds with "That guy is so dead. I'm gonna rip his lungs out!" After the flashback is over, the ghost of the week stabs Sam, and after making sure he's okay, Dean exclaims "That ghost is so dead. I'm gonna rip its lungs out!" May not make much sense, but it's still adorable.
Anna intervening to save Castiel from Uriel in "On the Head of a Pin". They don't agree with each other, they're never on the same side at the same time, and he has orders to kill her, but he's still her little brother and she'll stab you through the friggin' throat if you try to kill him. Aww? Tragically enough, it turned out to be her trust in Castiel that led to her eventualfate.
In "Jumping the Shark", even though he turned out to be a ghoul, the scenes with Sam teaching Adam to fend for himself are very heartwarming, showing that the connection between the two really is a bond between brothers.
In "The Rapture", Jimmy's reunion with his family. And later Castiel's: "Of course we keep our promises. Of course you have our gratitude." While gently running his/her fingers through his hair. And then Jimmy begs him to let his daughter go, because he doesn't want her to suffer as he did.
And after all their problems in Season 4 and even though they have a whole new set of problems in the next season, seeing them cling to each other's jackets like two scared little boys as Lucifer is about to rise is somehow very sweet.
When Raphael begins to attack Dean and Castiel: "Go. I'll hold them off." Oh, Castiel.
Oh, Castiel indeed. He has another one in On the Head of a Pin. "You can't win, Uriel. I still serve God." Possibly doubling as a Crowning Moment of Awesome.
In "Sympathy for the Devil", Demon!Bobby yells at Sam, and basically tells Sam that after all is said and done, he never wants to speak to his again. But after the demon is dead and Bobby (recovering in the hospital) is done giving the doctors and nurses hell (not literally)...
Bobby: I was awake. I know what I said back there. I just want you to know that was the demon talking. I'm not cutting you out, boy. Not ever.
While damn Tear Jerker-y, Sam and Jessica's reunion in "Free to Be You and Me" when they tell each other how much they miss each other. Except then Jessica starts giving him a Breaking Lecture and blaming him for her death and it's eventually revealed to be Lucifer manipulating his dreams.
It's laden with snark, but when a retired Sam calls Bobby to tip him off about demon omens nearby, we hear what Bobby really thinks of him as a hunter:
Sam: Yeah. So I just thought you might want to find out who's in the area and put a man on this.
Bobby: Okay, let me see if I can think of the best hunter who might be in the immediate vicinity ó oh, that'd be you.
Castiel's simple reason for refusing to help Anna destroy Sam.
"The answer is still no because Sam is my friend."
Admittedly, there wasn't much in "Dark Side of the Moon" that wasn't really angsty, but Dean's re-living of a moment when he got to hug his mom and comfort her was definitely an awww moment. Which was exactly why when Dean encounters her again later, and she starts verbally abusing him it became such a Tear Jerker.
Finding out that Ash and Pamela are happy up in Heaven.
In "Point of No Return" Dean is ready to say yes to being Michael's vessel. Bobby and Cas have given up on him but Sam keeps believing that Dean will do the right thing. Even when Dean points out he doesn't have that same sort of faith in Sam, Sam simply says, "You're still my big brother."
Later, Dean proves Sam right, even when he was on the verge of saying yes. What made Dean change his mind? He didn't want to let his little brother down who had so much faith in him.
Gabriel: Damn right they're flawed. But a lot of them try, to do better. To forgive. (beat) And you should see the Spearmint Rhino.
Many moments from the season finale, "Swan Song":
Sam quoting Dean from the pilot episode, telling him to go live a "normal, apple-pie life" after Sam's gone.
Kind of halfway between heartwarming and heartbreaking, but still: Chuck's narration of the history of the Impala, culminating in Sam overcoming Lucifer's hold over him as he looks at the Impala and remembers all the times he and Dean have spent together.
Chuck: It never occurred to them that, sure, maybe they never really had a roof and four walls but they were never, in fact, homeless.
After being told that there's nothing he can do to save Sam, Dean replies, "Well then I ain't gonna let him die alone." Also a bit of a Tear Jerker.
Lisa temporarily embodying every fangirl watching the show by telling Dean it's okay and comforting him as he cries in her arms.
Any scene of Dean's civilian life with Lisa and Ben in "Exile on Main St."—hell, the whole season! They very clearly love him and he very clearly loves them back.
Sam and Dean choosing a name for the shifter baby in "The Third Man". Sam chooses John, showing that he's forgiven his father, while Dean picks Bobby, cementing Bobby as his father figure.
"All Dogs go to Heaven". Someone has been planting skin-walkers with various families, so they can all turn their families into 'walkers at a given signal, forming an army. The guy who's been killing people? A 'walker who's come to care about his family. Just like a real dog.
"Like a Virgin" is full of them. Sam and Dean hugging, and then Sam and Bobby. Castiel, who used to call Sam an abomination and "the boy with the demon blood", wanting to hug him counts too.
In "The French Mistake," Sam and Dean are catapulted into our world, where Supernatural is just a TV series, there are no monsters, and they're living the lives of the actors who portray them on television. Throughout the episode, they constantly try to return to their own world. But at one point, Dean wonders if Sam even wants to go back to their old lives, seeing as this life is pretty good in comparison. Sam's response is that this life isn't appealing at all, because in this world they don't mean anything. Even worse? Sam and Dean aren't even BROTHERS! That's right- the thought of spending the rest of their lives as celebrities holds no appeal to them because they wouldn't even be related anymore.
"Mommy Dearest": The boy keeping his head and looking after his younger brother even when the entire town is in chaos, and the obvious parallel to Dean and Sam.
In the premiere, after he seemingly dies and comes back to life, Castiel repeatedly tells Dean that he will prove that he can be trusted, and he will do anything to make up for his recent behavior. It is clear that Dean is touched, even if he tries to cover it up. Aww, Look! They Really Do Love Each Other!
When Castiel goes to Sam, Dean, and Bobby for help, he's in pretty awful shape. Bobby and the Winchesters could've just hauled him up to Purgatory without an ounce of sympathy, but they don't. Despite everything, they treat Cas very gently as they prepare the gates: telling him to hang in there, touching his shoulder, helping him stand. The fact that they still care enough about him to do that is quite sweet.
Sam steadily starts to lose his mind in "Hello, Cruel World" and thinks that he's still in Hell with Lucifer, with the past season being an elaborate Mind Screw to torture him. Dean sets him straight.
Dean: Hey. I am your flesh-and-blood brother, okay? Iím the only one who can legitimately kick your ass in real time! You got away. We got you out, Sammy... Believe in that! Believe me, okay? You gotta believe me. You gotta make it stone number one and build on it. You understand?
Sam: Yeah. Yeah, okay.
Ghost!Jo and Dean in "Defending Your Life", even when she's being forced to kill him. When Sam manages to break the spell, she smiles softly at Dean and tenderly cups his cheek before vanishing.
Ellen's message to Dean from beyond in "The Mentalists": If he doesn't tell someone how bad things are, she will kick his ass from beyond. Gone two years and still watching out for the boys. Is there any question that she's their surrogate mother figure?
"Death's Door"—"As fate would have it, I adopted two boys and they grew up great. They grew up heroes!"
Hell, almost all of Bobby's flashbacks that weren't Tearjerkers were these. Including playing catch with Dean when John wanted him to practice shooting. Later calling John out on his behavior around the boys saying that they are kids.
And the revelation that his happiest memory is actually simply sitting and drinking beer, while the brothers childishly argue what movie to watch.
"Plucky Pennywhistle's Magic Menagerie": Sam, knowing all that he's been through, taking one for the team to let Dean have a good laugh.
Something about Sam giving Dean the slinky.
Consider Sam's situation in "The Born-Again Identity": he's sleep-deprived, slowly going insane, trapped in a psych ward and dying. Yet he still takes the time to help a girl he's only just met. Someone hug the man, please.
Dean returning the amnesiac Cas's trench-coat to him.
Cas makes good on the promise from the premiere by taking on Sam's madness in order to save his life. Doubles as a major Tear Jerker.
Meg takes care of Castiel after he absorbs Sam's madness and loses his mind. She's very gentle with him, more than either Sam or Dean, and she seems to truly care for him. Maybe demons can change without being cured.
Crossing over with Tear Jerker, as Bobby's vengeful spirit is calmed and he comes to peace with his death, the boys promise that while they will kill Dick Roman for him, it will be for justice and not revenge.
In the flashback sequence of "What's Up, Tiger Mommy?" Dean and Cas' reunion in Purgatory. The hug, Cas' explanation for leaving Dean alone at the end of the previous season, and Dean's declaration of "I'm not leaving without you." It was incredibly heartwarming to see them reconcile after everything they'd been through in previous seasons.
Crossed with Crowning Moment of Funny is the revelation in "Southern Comfort" that Garthofallpeople is now taking up Bobby's mantle in helping other hunters, as well as trying to talk Sam and Dean through their issues, and seems to be pretty damn good at it. Dean comes to accept this despite his initial displeasure with the situation.
Dean finally, finally having someone (in this case Cas) tell him in "A Little Slice of Kevin" that he doesn't need to save everyone, and that he's not at fault for the self-destructive actions of those he loves.
Castiel pulling out a chair and sitting down next to Fred Jones (the psychic) near the end of "Hunteri Heroici", particularly his smile at the look of happiness on Fred's face as the old man listens to "Ode to Joy".
Dean's little bonding moment with Charlie in "LARP and the Real Girl" over all the little nerdy things at their camp. There's also the part where he assures her that who she is outside of LARPing is a real hero for everything she did for them and everyone on earth.
Sam and Dean LARPing at the end of the episode could fit here as well. As they finally decide to have some fun and help out Charlie.
Henry admitting he was wrong about hunters and telling Sam and Dean that as long as the Winchesters are still alive, "there's always hope," near the end of "As Time Goes By". He then dies clasping their hands. There's also both Dean and Sam standing up for their father after their years of berating him.
8.16 - "Remember the Titans"
The final minute or so of the episode when Dean prays to Cas was a moment that I found very heartwarming because it's a reminder that Dean, who doesn't pray because he considers it "the same as begging," is praying not to God, who he doesn't have faith in, but to Castiel whom he does have faith in.
From "Pac-Man Fever":
Charlie: I love you.
Dean: I know. (they hug, and Dean kisses her hair when they pull away)
And generally any interaction between Dean and Charlie. They go on a shopping trip together (with Dean playing the role of the gay best friend by giving a yes or a no to her different outfits!), leave Sam at the batcave to investigate, and Dean reacts most violently to the thought that Charlie is the djinn's latest victim. He takes dreamroot to try and save her and convinces her quite gently, given the circumstances, that she needs to let go of her mother.
Dean's protectiveness toward Sam in this episode is also quite sweet, in an angry-out-of-love kind of way. This is the same guy who berated Sam for giving up hunting in the same season, and he sees how disheveled Sam is and demands he stay home and get some rest, and gets pissed when Sam comes along anyway.
From "Clip Show", there's Castiel going shopping after the Winchesters leave him to investigate Max. He grabs a bunch of stuff he thinks Dean would like (to get back into his good books), like toilet paper, beef jerky, a six-pack of beer, and a copy of Busty Asian Beauties. Then there's this gem:
Castiel: Where's the pie?
Cashier:[annoyed] I think we're out.
Castiel:[grabs his shirt and drags him across the counter] You don't understand. I NEED. PIE.
Dean's speech to Sam from this season finale—and the hug that follows.
Dean: Hold on! You seriously think that? Because none of it, none of it, is true. Look, man, I know Iíve said some junk that set you back on your heels, but, Sammy, címon, I killed Benny to save you. Iím willing to let this bastard and all the sons of bitches that killed mom walk because of you. Donít you dare think that there is anythingópast or presentóthat I would put in front of you. It has never been like that. Ever. I need you to see that. I'm begging you.
Crowley regaining his humanity.
Crowley: Band of Brothers? The Pacific? None of this means anything to you? All those motels, you never once watched HBO? Not once?Girls? You're my Marnie, Moose. A-and Hannah—she just—she needs to be loved. She deserves it. Don't we all? You, me—we deserve to be loved. I DESERVE TO BE LOVED! I just want to be loved...
From the premiere:
While praying for Sam (itself a CMOH), Dean tries to reach Cas. He tells him that it doesn't matter what he did, they'll work through it together. Compare to Dean only a few episodes earlier, upset at Cas for not trusting him with the tablet.
When Cas calls Dean, the first thing he does is try to explain that Metatron tricked him, so that Dean knows he didn't cause the Fall on purpose. Dean doesn't care - he's more worried about whether or not Cas is okay.
Dean is asked several times where Cas is by the other angels, and not once does he betray him.
The truck driver is a walking CMOH. He picks up a guy off the side of the road who's muttering about angels, drives him to a gas station, and gives him money for food, no questions asked.
Death of all entities has a major one in his interactions with Sam, where he reveals that he considers it an honor to collect Sam's soul due to all the good he has done, and when Dean comes up with a plan to save him he allows it despite his well noted dislike of the natural order being tampered with.
From the second episode "Devil May Care"
Dean's speech to Kevin as the latter tries to leave the safe bunker. After all they've been through, Dean considers him a part of his family.
From the third episode "I'm No Angel":
This exchange after Cas is brought back from death was really heartwarming in its simplicity:
Dean: Never do that again.
Castiel: All right.
Characters that are resurrected have a brief mental bleed-over of their personal Heavens, which in the Supernatural universe consist of their happiest memories, before they realize they're alive. What does Cas say right as he's waking up?
The one night of bliss Castiel experienced with April (before the reveal, the interrogation, the torture and the ganking). That little Cheshire cat smile, while easily associated with Misha Collins's happy-go-lucky persona, was such a rare sight for his character before this episode.
From the sixth episode, "Heaven Can't Wait":
Castiel awkwardlysinging to an infant girl he was babysitting until she calmed down, walking and bouncing her in his arms all the while. Oh, and the song? Believe It or Not by Joey Scarbury.
The twelth episode "Sharp Teeth":
Dean telling Garth, who is now a Werewolf, that he has found happiness with his wife and should hang on to that, and to retire as a hunter, and admits that Garth was right, it doesn't matter where happiness comes from. And then finally giving Garth a hug, instead of Garth giving him one.
And a bonus: Dean is admitting that the Werewolves of Garth's pack are good people. His time with Benny really did change his attitude towards monsters.
Castiel telling the dead angel Rebecca that he respects her for trying to find a new way for the angels, even if she failed and died for it.
Ghost Kevin telling Sam and Dean that their fighting is stupid and that they are both still alive and have each other, and that they should make-up. Averted however when he leaves and Sam and Dean go right back to ignoring each other.
Brotherly CMOH's haven't been easy to come by recently, but Sam and Dean's "Weechester" memory can count. First off, Sam makes reference to "a baby chimp falling out of the tree," which apparently reminds Dean of five year old Sammy, which is adorable in and of itself. The memory itself is also cute, with a young Sam breaking his arm diving off a roof pretending to be a superhero, because "Dean did it first!" (as Sam still protests in the present day). Finally, the adult and at this point very emotionally estranged brothers smiling and laughing over this happy memory seals the deal.
9x17 - "Mother's Little Helper"
The fact that so many years later Sister Julia remembers the people who saved her life and her soul.
Sister Julia: I was so scared. I prayed and prayed, but God didn't answer my prayers. Henry and Josie did.
9x18 - "Meta Fiction"
This troper found that Gabriel's telling Cas that they have a lot in common was quite nice. He's letting Cas know that there's at least one other Angel out there who agrees with what he believes about free will.
9x19 - "Alex Annie Alexis Ann"
The entire plot with Annie Jones and Sheriff Mills. The Sheriff refusing to believe that Annie is evil, helping her see the truth behind her vampire "family" and at the end taking her in as a daughter. Both of them help each other move past the darkness in their pasts.
9x21 - "King of the Damned"
Crowley's newfound feelings for his son Gavin, the two of them bonding over Gavin technically being the "Prince of Hell" and Gavin actually managing to bargain with Crowley, and at the end allowing Gavin to escape Sam and Dean and live a real life in the present, rather than let them send him back to die in a shipwreck in the past. Crowley's human blood addiction helped him find the feelings for Gavin that he didn't have when he was human. Without a doubt the nicest thing Crowley has ever done, because he didn't get anything back from it. He did it because he wanted to.
9x22 - "Stairway to Heaven"
Sam telling Castiel that he belives he isn't responsible for the angelic suicide-bombings, and affirming that he trusts Cas, especially given that Dean at the moment doesn't.
Castiel refusing to punish Dean, even knowing it will cost him his army, he still won't harm his best friend.
Dean telling Castiel that he does trust him after all, and that the three of them will take down Metatron together;
Dean: Cas, you just gave up an entire army for one guy. No, there's no way that you blew those people away.
Castiel: You really believe we three will be enough?
Dean: We always have been.
9x23 - "Do You Believe in Miracles?"
Gadreel joining Team Free Will after he realizes the truth behind Metatron. Joining with Castiel and travelling to Heaven to stop Metatron they end up captured and Gadreel makes his Heroic Sacrifice to free Castiel, telling him that what matters is protecting humanity as God wished them to do. And he takes a moment to warn Hannah, an Angel he's never even met and who could actually be a fervent Metatron supporter for all he knows, to take cover for her safety.
Gadreel: I sat in this hole for thousands of years thinking of nothing but redemption, of reclaiming my good name. I thought of nobody, no cause other than my own.
Castiel: You've been redeemed my friend.
Gadreel: The only thing that matters in the end is the mission: protecting those who would not and cannot protect themselves. The humans. None of us is bigger than that, we will not let our fears, our self absorption prevent us from seeing it through. Not anymore.
Castiel: No, no of course not.
Gadreel: Move to the other side of your cell Castiel, and keep your head down. When they say my name, perhaps I won't just be the one who let the Serpent in, perhaps I will be known as one of the many that gave Heaven a second chance. Run sister.
Dean telling Metatron that ultimately, the entire reason he is hunting him is because Metatron had Kevin murdered. Dean really did care for that kid.
Sam coming to Dean's aid, too late sadly, and carrying him out of the warehouse. And at the end Sam refusing to allow Dean to die that pointlessly and preparing to make another deal to save him.
Dean finally feeling proud of himself for what he and Sam have achieved in their lives, a list of heroism that most would admire;
Dean: Iím proud of us.
YMMV but Crowley returning to see Dean one last time and then helping him open his eyes, revealing Demon!Dean. This troper got the sense that Crowley really does consider Dean a friend in a way, and here he was helping a friend.
In Soul Survivor, Dean becomes human again.
Episode 5 - "Fan Fiction"
Chuck Shurley aka. GOD went to see the play of Supernatural that Marie put on in this episode and he liked it. The whole episode was a love-letter to the fandom, but the final scene left was jaw dropping. There could be no greater heart-warming end to the episode than to have GOD HIMSELF appear at the end and say he liked the play that Marie, a dedicated fan of the Supernatural book series, produced.
The cast of Supernatural: The Musical singing Carry On Wayward Son together, and Sam and Dean watching it together. Gives you the hope that perhaps one day Sam and Dean will be able to find rest and peace for themselves.
The return of the Samulet, a wooden copy of it at least, and Dean hanging it up in the Impala. A sign that Sam and Dean really are working to rebuild their relationship.
Episode 7 - "Girls, Girls, Girls"
Hannah giving up her vessel so that she can return to her husband, and saying that she believes the humans must now come first. And after that Caroline's husband welcoming her back without question.
Episode 9 - "The Things We Left Behind"
Castiel trying to atone for wrecking Claire's life by taking her father as his vessel. He refuses to abandon her through the entire episode, despite multiple people telling him it might be for the best.
Castiel telling Dean that he considers Dean a good role model, despite the fact that Dean doesn't.
Dean's story about sneaking into a club in New York;
Dean: So I get there, I sneak in, and it is nuts. I mean people are drinking, and they're smoking, and they're snorting whatever. There's a 500 pound guy on the stage with mohawk just screaming. My mind is blown I don't even know what to do. Then this girl walks up, and she's 'Hey why don't come over sit down with me and my friends at this table,' 'yeah, alright.'
Sam: Yeah and they get him drunk. First time.
Dean: But not fun drunk, I'm not quite sure what was in that stuff, but the room starts to spin, and I feel like I'm going to puke forever. Right about that time, I hear him. 'Dean Winchester.' My old man, I don't know how but he found me. And now I'm really freaking out, because he's just standing there not saying anything, and I look around everyone else is freaking out too in fact no one is looking him in the eye, then finally this one guy with like a safety pin in his nose and a 'kill everything' tattoo looks up and he says 'sorry sir.' Yeah, 'sorry sir' heh. John frickin' Winchester.
Both Sam and Dean affirming that despite all the problems they had with him, they do in fact love John. Dean's "With everything I had," was especially heartwarming, considering what he said only seven episodes ago.
The fact that despite complaining about being dragged out on what Dean does not consider an emergency and Sam's reservations about the situation, the Winchester's immediately drop everything when Castiel says "I need your help." He's been there for them so many times, and all he has to do for them to be there for him is ask.
After all the moments of painting John in a bad light this officially confirms that John may not be a perfect parent but he tries to raise Sam and Dean the best he could.
Crowley saving Rowena from Gerald at the end of the episode. He still cares a little bit about his mother, though whether or not that is a good thing for him has yet to be seen.
Castiel coming to rescue Claire from the thug intent on raping her. And once they get into the Impala and she starts shaking he hugs her, and shields her eyes as they come across Dean's massacre, like a father would.
In "Frontierland", Dean makes a reference to Star Trek IV: The Voyage Home and Bobby says that he only watched Star Trek: Deep Space Nine. The line was originally for TNG, but because Jim Beaver's late wife had portrayed the recurring character of Ishka, Quark's mother, on DS9, he asked that it be changed.
One Big Name Fan of the Supernatural fandom, known as Sashi, was diagnosed with endometriosis. Her friends, unable to take her not asking others for help and hating to see her suffering any more, started a donation fund on Tumblr to help called "Donate For Sashi". It was rotated around Tumblr and after a day they managed to collect over $7000 in Sashi's paypal account. One person in particular asked Supernatural star Kim Rhodes to rotate the donation fund and spread the news about it, but Kim Rhodes did one better and actually asked for her information so that she could refer Sashi to a doctor in California who would actually work with her on the money issues. Crowning Moment of Heartwarming for the fandom and Kim Rhodes.
In "The Girl With The Dungeons and Dragons Tattoo," Charlie psyches herself before a dangerous mission by saying she's gonna "Kick it in the ass." This was Kim Manners, departed producer and director's, catchphrase.
It's also written on the mix tape Dean plays just before confronting his possessed brothers in an attempt to stop the Apocalypse.
Also the last thing Ellen says to the boys before a Taking You with Me attack on some hellhounds.
In "Three Years Ago," the episode takes place during Sam's time in college and one of the targets is Jessica. When John finds this out, he becomes even more concerned about the case and obviously is motivated by Sam's involvement more than anything. This also goes for Dean when he finds out. The episode ends with them watching Sam and Jessica happily walk off, unaware that John and Dean had just saved their lives, and looking very proud at how much Sam's grown.