Any emotional moment involving Walter Bishop is likely to be this at least for some, partly due to the complex character interaction but mostly because of John Noble's performance.
That scene between Walter and Peter at the end of "Grey Matters." (S02 E10)
Peter calling Walter "Dad." Made extremely poignant by the following episodes.
When Peter sang Row Your Boat to Walter at the end of "The Same Old story" especially since he had been short and dismissive of him for the last two episodes. D'aaaaw!
Broyles' anger at the way Harris treated Olivia. Considering that he started out hating Olivia because she put Harris in prison for sexual assault, his anger at him is a great showing of him becoming a Papa Wolf.
Peter playing with Olivia's niece Ella in "The No Brainer". It's one of those small, adorable moments that's a real pick-me-up after a really scary one.
The end of "The Transformation" (S01 E13). John and Olivia's goodbye/proposal. He really did love her after all. *sniff*
"I've thought of a hundred reasons why you should come back. To fight the shape shifters, to look after Walter, to save the world. But in the end you have to come back... because you belong with me."
The scene in "Subject 13" when Peter and Olivia first see each other. They don't know each other from Adam, both catch sight of each other through the glass, and you can practically see little anime hearts behind them. At this point, they're both just nine. It's just the cutest darn thing.
The scene with Peter and Olivia in the tulip field was simultaneously heartbreaking and adorable. You just wanted to huggle them both.
Walter threatening Olivia's abusive douche of a stepfather. Considering he spent the better half of the episode performing questionable (read: illegal and somewhat cruel) experiments on her, it was nice to see that he cared. It was also nice to see the dick in question looking terrified.
Four words that will move any fan of Charlie Francis to tears. "You're gonna be fine."
Most of "Bloodline."
Lincoln's "I love you," the look of devastation when he thinks Fauxlivia is gone and the Manly Tears he sheds when she wakes up.
Henry the Cabbie's unwavering loyalty to our Olivia.
The look of pure adoration on Fauxlivia's face when she holds her baby.You may hate her (in fact, I still don't like her) but I'll be damned if that woman didn't drag herself out of the very depths of scrappy heap after making Lincoln promise to save baby Bishop even if it meant her own life.
A subtle one in 3x19. In the pilot episode, Peter called Olivia insane for taking large amounts of LSD to save John Scott. In this episode, he does the same thing and his only concern is that his actions may somehow harm Olivia.
And in The End Of All Things he does it again to save amber!Olivia. Only this time, he enters the mind of a dying September.
Peter tells Walter that he (not Walternate) is his real Dad in 3x22. Made into a real Tear Jerker by later events.
Any scene where Olivia is at home with her sister and niece. It's just a lovely, humanizing layer to a character that could have been a really boring, on-note hard-ass in the hands of lesser writers.
The ending of "One Night In October."
Broyles: At the risking of sounding sentimental, I've always thought that there were people who leave an indelible mark on your soul. An imprint that can never be erased.
Alone in the World when Walter is begging the boy to break it's connection with Gus so he will not die with it. Eventually he manages to get through the boy at the last possible moment and for Amber Timeline Walter he manages to save the boy this time, all while Astrid is in the back ground crying because she knows losing another boy would have destroyed Walter and that he managed to find something near absolution for Peter's death by saving Aaron.
The pep talk Walter gives Olivia in 3x21. "I wish you could see yourself the way I see you. You have no idea how extraordinary you are."
Astrid in "What Lies Below", refusing to abandon either Peter or Walter in a quarantined building despite having just been told that everyone in the building will be killed:
Astrid: Walter will figure something out. We're going to be fine.
Peter finding out in "Back to Where You've Never Been" that this timeline's Walternate is not who he knows from his own timeline, and is doing just as much to try to stop what's happening as "our" Walter.
And at the end of the next episode, after our Walter comes to Peter to say he'll help Peter cross back over to his original timeline, Peter says: "I just spent the last several days with the other Walter, and I was very surprised to learn that he is not the man that I thought he was. But I am not at all surprised to learn that you are."
Astrid getting Alt-Astrid coffee. She gets so excited and has the most adorable smile on her face.
Astrid's relationship with her alternate in general. She calls her "sweetie" at one point.
Ella's ending to Walter's story in "Brown Betty" .
(adds her own ending to Walter's heartbreaking story) "...and Peter looked inside Walter's eyes and realized there was still goodness inside him. So Peter took his special heart, and with all his might, he split it in two. And the heart was so magical that it still worked. And together, they made goodness, and lived happily ever after. The End."
September: There is no scientific explanation. But... I have a theory. Based on an uniquely human principle. I believe you could not be fully erased because the people who care about you would not let you go. And you... would not let them go. I believe you call it love.
A bit of a heartwarming in hindsight moment, but most of Nina's scenes with Olivia in Season 4 were tainted by everyone thinking she fostered a teenage girl for the sole purpose of drugging her against her will and was working with David Robert Jones to kill billions of people. She wasn't. Upon rewatching, they're some of the most touching scenes in the series.
Olivia: I thought I was going to die today. And one of the things that I kept thinking was that you... you wouldn't know how I felt. You're the closest thing I have to a mother and I love you.
This scene is followed by Nina fussing over Olivia and cooking her soup.
August, who went rogue from the Observers and made it his sole mission to save the life of one girl. Despite the other Observers repeatedly declaring the girl to be unimportant, he risked his own life, simply because she was important to him.
Olivia taking the tech from Peter's bloody hand and replacing it with "the bullet that saved the world."
In Black Blotter, when the heavily tripping Walter manages to remember the secret password ("Black Umbrella"), the green fairy hallucination appears briefly and applauds. Walter bashfully smiles to her.
Nina Sharp's undying loyalty to Olivia in 5x10. There is no doubt that she loves her daughter and that Olivia, despite forgetting her childhood, loves her too.
Peter comforting a distraught Walter and Olivia after Nina's death.
Walter being determined to go with Peter and Olivia to make sure Nina is alright, despite the danger. In the entire episode, this is the only point the Walter we know and love shows himself.
Whatever visions Michael showed Nina isn't revealed, but whatever it was, it worked. While she was fully prepared to give up her life to save the team, she was terrified until that moment.
Michael gives Walter his memories from the original timeline.
Walter:I remember when you came to me in St. Clair's. My first words... "I thought you'd be fatter". I remember the night I was up late making a peanut butter sandwich and you slipped and called me Dad. The feeling of joy that gave me. And the terror... before you stepped in the machine. I told you that I had never been good at letting you go and you said-
Peter:This time you're gonna have to. What is this boy? How can he do this for you? Enable you to see a life you didn't live?
Walter: Not sure. But I feel it.
Peter: Do you remember the plan?
Walter: No. No idea.
Peter: But that doesn't make any sense! Why would he give you back all those memories and not give you back the plan?
Walter: I don't know. Peter... before I met him, I didn't think it was possible to love you more. But now... knowing what we've been through... and everything we've had... I do.
Cue the most adorable Man Hug ever shown on television. Ever.
Donald and Michael. Every scene with those two.
Donald's speech to Walter in the finale about how he came to love his son.
The entirety of Donald's friendship with Walter. They watch musicals together.
The moment when Donald finds out that Walter, Peter and Olivia are alive. He looks so happy.
"Truthfully, it wasn't much of a punishment. I have always held this era in the highest regard."
Fauxlivia and Lincoln are happily married. And they managed to have a son despite Fauxlivia's VPE.
Fauxlivia and Olivia hug. No hard feelings apparently.
Also the warm hug between Lincoln and Olivia- both seem very glad to see their old friend and partner.
Lincoln feeling guilty about leaving his universe and Olivia reassuring him.
Olivia: You deserve all the happiness that you got.
Walter and Astrid's final scene with Gene the cow, and Walter finally getting Astrid's name right. Also a MASSIVE tearjerker.
“You are my favorite thing, Peter. My very favorite thing.”
The ending. Walter gives up the chance of seeing his family ever again so that Etta would live and that the world would be safe. The series finishes with Peter picking up Etta at the park, taking her home for a bath and then getting a white tulip in the mail from Walter.