In "Beyond the Sea", Mulder and Scully had a sweet moment when Mulder stopped her and expressed his sympathy over her father's death.
The ending of "Beyond The Sea".
Mulder: Dana... after all you’ve seen, after all the evidence…why can’t you believe? Scully: I’m afraid. I’m afraid to believe. Mulder: You couldn’t face that fear? Even if it meant never knowing what your father wanted to tell you? Scully: But I do know. Mulder: How? (beat) Scully: He was my father.
Scully's passionate speech to Mulder in the first season episode "E.B.E". is so unexpected coming from her but also completely natural after all they've been through together. The next scene reveals that Mulder has agreed with her in his own crazy way. It also marks the point where Scully becomes the only person Mulder trusts.
Scully: "I have never met anyone so passionate and dedicated to a belief as you. It's so intense that sometimes it's blinding. But there are others who are watching you, who know what I know, and... *beat* Whereas I can respect and admire your passion, they will use it against you. Mulder, the truth is out there. But so are lies."
The scene in the car in "Tooms" was sweet. It forged their friendship and sealed mutual trust.
Scully: Mulder, I wouldn't put myself on the line for anybody but you.
"Little Green Men" is full of heartwarming moments. Mulder records everything he finds on audiotape to send back to Scully, and as the action heats up, they go from professional to personal, ending with this quote:
Mulder: Deep Throat said "trust no one." And that's hard, Scully. Suspecting everyone, everything, it wears you down. You even begin to doubt what you know is the truth. Before, I could only trust myself. Now, I can only trust you... and they've taken you away from me.
And at the end of "Little Green Men", when Mulder is trying to play that audiotape for Scully only to find it's been wiped.
Mulder: It should be right here. The entire tape is blank.
Scully: You know, an electrical surge in the outlet during the storm may have degaussed everything, erasing the entire tape. You still have nothing.
Mulder: I may not have the X-Files, Scully, but I still have my work. And I've still got you. And I still have myself. (Scully squeezes his hand in support.)
Maggie Scully and Mulder have a heartwarming moment in "Ascension". When Mulder tries to give Maggie Dana's cross necklace, the only thing he found of her at the abduction site, she promptly hands it back to him. She shows her support and faith in Mulder not just as an investigator, but as her daughter's partner and someone who cares about her.
Mulder: Don't you want it?
Maggie: When you find her, give it to her.
Something implied but never directly touched upon during Scully's abduction arc is in the interesting friendship Maggie and Mulder form during this time; it's implied that they supported each other through it. Between "Ascension" and "One Breath" Maggie goes from calling him "Agent Mulder" to "Fox", which almost no one calls him. He is there when Maggie views the headstone she ordered for Dana, and all through the horrible news in "One Breath". She even tells Mulder that he is welcome to sit with her and Melissa after they take Scully off of life support. She also calls him from the hospital when she's found, and either she or Melissa called him later in the episode to tell him that she had come out of her coma. This connection comes up a couple more times in the series, most notably in the episode "Wetwired".
Scully in "The Host" when she says she would consider it more than a professional loss if Mulder decided to leave the Bureau.
"One Breath" is one big Tear Jerker crossed with a crowning moment of heartwarming. Start with Captain Scully telling his daughter it's not her time to die. Continue with Mulder returning Scully's cross to her. And Scully telling Mulder she "had the strength of [his] beliefs".
There's a tiny one at the end of "Firewalker". It's the first case that Scully is on after coming out of her coma, and she insists on participating despite Mulder's initial protests. He tries to hide his concerns, and deflects every "I'm fine, get over yourself" from her through the whole episode. Near the end, she finds herself handcuffed to a girl who is about to have a plant climb out of her throat and spew fatal pollen spores everywhere. She throws the girl into a locker—still handcuffed—as the plant finally takes over. Mulder comes rushing in, having only figured out that he'd left her alone with this girl a few minutes before, completely terrified. He can't do much more than say her name and drop down next to her on the ground. Given what had just happened to her a few episodes before, Scully immediately recognizes his terror and her first instinct is to reassure him that she's fine, and to nod in affirmation when his face clearly says "You sure?" Sweet moment.
Scully breaks down her walls and accepts Mulder's comfort at the end of "Irresistible".
A small one from "Fresh Bones". Mulder and Scully arrive at a graveyard to arrest a suspect. Scully is feeling ill from the effects of voodoo magic (the prevalent theme of the episode), so stays a few minutes longer in the car while Mulder goes on ahead. A few minutes later Mulder also ends up the victim of voodoo, in pain and collapsed on the ground. When Scully catches up with him and helps him sit up, the first words out of his mouth are to ask if she's okay.
From "End Game": Scully's smile when Mulder wakes up is really wonderful, very lovely and very heart-warming. Mulder and Scully's dialogue is heart-felt by both of them.
Mulder: I'm sorry, I, uh... I couldn't let you risk your life on this. Scully: Did you find what you were looking for? Mulder: No. But I found something I thought I'd lost. (looks at her, then takes her hand) Faith to keep looking.
Scully taking care of Mulder while he's sick in "Anasazi". Even though he's a total jerk to her thanks to the water in his apartment being laced with LSD.
Deep Throat and Bill Mulder appearing to Fox Mulder in "The Blessing Way".
Mulder comforts Scully after her sister dies at the end of "Paper Clip".
Scully goes to Mulder's father's funeral to tell his mother that Mulder will be fine. She and Mulder talk about it later:
Scully: I went to your father's funeral. I told your mother that you were going to be okay.
Mulder: How did you know?
Scully: I just knew.
Mrs. Scully defends Mulder from Scully, who has been given paranoia, induced by subliminal messages, in "Wetwired". The show-down between Mulder and Scully was amazing if painful to watch. Mulder's absolute trust in Scully, even tough he saw what other victims did and his strong wish to help her... It is so much like them. Mrs. Scully's support and trust feel great.
Mulder: Scully, you are the only one I trust.
From "The Field Where I Died": Scully'd do it all again, no regrets. Except for that Flukeman thing... she could live without that.
Mulder reuniting with Scully in "Terma". He feels extraordinary lucky that he saved his life and his limbs.
Mulder: I can put my arms around you — both of them.
The entirety of the episode "Memento Mori".
Mulder surprises Scully with a celebration of her birthday at a bar in "Tempus Fugit". Scully is moved because he never remembered her birthday. Mulder tries to belittle it by claiming that this is how he likes to celebrate it — every four years because then it's like dog years. It's all very sweet with a little strawberry cupcake or ice cream with a sparkler, the happy birthday song by the waiters and a little present which is a gold Apollo 11 key chain. It's also a bit of a tear-jerker because it happened after Scully had been diagnosed with cancer.
Scully singing Three Dog Night's "Joy to the World" to a concussed Mulder in "Detour", which gets an adorable Call Back when Scully amends the song for her baby: "William was a bullfrog..." in the episode "William".
Mulder and Scully having an impromptu slow-dance at the very end of the "The Post-Modern Prometheus". That the episode itself was something of a Moment of Awesome for the season or series which earned it seven Emmy nominations and a parade of rave reviews enhances the good feeling. David Duchovny would go on to say that whatever came after, for him, that one moment would always remain his favorite.
"Folie à Deux", and Mulder telling Scully she's his "one in five billion".
An exchange from the autopsy scene in "Trevor", which is both funny and heartwarming at the same time. Scully has a Mulder moment, and Mulder is both pleased and amused.
Scully: Spontaneous human combustion. Mulder:(nearly breathless in disbelief, as if he was complimented in the sweetest way ever) Scully! Scully: Well, isn't that where you're going with this? Mulder: Dear Diary, today my heart leapt when Agent Scully suggested spontaneous human combustion. Scully: Mulder, there are one or two somewhat well-documented cases. (Mulder says nothing but he keeps nodding thoughtfully) Scully: Mulder, shut up. (Mulder smiles and gives Scully a somewhat confused look)
End scene of "Milagro".
"The Unnatural" is just one long crowning moment of heartwarming. We dare you, we double dare you not to feel any emotion other than pure heartwarmth at the fate of Josh Exley. The shippers will appreciate the adorable Mulder-Scully interaction in the office and the baseball lesson at the end.
Mulder: Scully, I was like you once — I didn't know who to trust. Then I... I chose another path... another life, another fate, where I found my sister. The end of my world was unrecognisable and upside down. There was one thing that remained the same. You... were my friend, and you told me the truth. Even when the world was falling apart, you were my constant... my touchstone. Scully: And you are mine.
Scully comforting Mulder after his mother's death in "Sein und Zeit".
When Mulder finds Samantha's diary. While much of it describes horrible tests and the pain she went through, one page talks about memories. She believes the doctors have removed hers, but "not all of them" and she thinks she remembers that she had a brother, one with "brown hair, who used to tease me". She goes onto to say that she hoped one day Mulder would find the diary, and know that she wished she could see him.
The seventh season episode "Requiem" has the totally adorable cuddling scene. Mulder and Scully are lying together in a classic spooning pose. There is no awkwardness.
Mulder agrees to be the father of Scully's baby in "Per Manum".
Skinner in "This is Not Happening". Especially when Scully showed up at his door in a panic in the wee hours of the morning and he stood outside comforting her and reassuring her that Mulder was not dead.
The young agent Leyla Harrison's eager approach and general cuteness in "Alone". Just the fact that she is a fan of Mulder and Scully feels amazing. Was she the only one from their peers who respected their career and who understood what that had been doing? The penultimate scene of the episode is beautifully done: She's in a hospital room and Mulder and Scully visit her, giving her the Apollo medallion that Mulder once gave to Scully, which she re-gifted to Doggett. Agent Harrison's sheer joy leaves her nearly speechless: "No way... This means... I can't tell you what this means to me." She then asks a very good question, wondering how they got from Antarctica to Washington, DC because nobody had known about that trip and because there had been no gas in Mulder's Sno-cat. Mulder and Scully's heart-warming argument ensues. Too bad we never get to hear the answer. It gets even more heartwarming when you hear the backstory behind Leyla's character: Leyla Harrison was a real person, a well-known X-Files fanfiction author, who died of skin cancer in February 2001.
Mulder and Scully being cute with Baby William at the end of "Existence".
No matter how you feel about the way the series ended, it's hard not to be moved by the final scene in the series finale as Scully comforts Mulder and they look to the seemingly bleak future with renewed hope.
Scully: Why would I accept defeat? Why would I accept it, if you won't? Mulder, you say that you've failed, but you only fail if you give up. And I know you - you can't give up. It's what I saw in you when we first met. It's what made me follow you... why I'd do it all over again.
Mulder: And look what it's gotten you.
Scully: And what has it gotten you? Not your sister. Nothing that you've set out for. But you won't give up, even now. You've always said that you want to believe. But believe in what Mulder? If this is the truth that you've been looking for, then what is left to believe in?
Mulder: I want to believe that... the dead are not lost to us. That they speak to us... as part of something greater than us - greater than any alien force. And if you and I are powerless now, I want to believe that if we listen, to what's speaking, it can give us the power to save ourselves.
Scully: Then we believe the same thing.
Mulder: (after climbing onto the bed and taking her into his arms) Maybe there's hope.
From the second film, there's Skinner hugging Mulder to keep him warm.
Mulder's speech to Scully in the hallway of his apartment building in "Fight the Future", reassuring her that he has always appreciated her and that he needs her.