From PK Wars, Crichton and D'argo's final exchange
Crichton: You're the closest friend I have.
D'argo: You could've done better.
Crichton: Not in the entire universe.
From PK Wars, when Rygel gently tells Aeryn that the baby will be safer with him on his hover-chair as Moya swoops in with a grappling net. She reluctantly hands the baby over on John's insistence, and Rygel rocks him gently and pulls off the retrival without a hitch.
Oh, and in season three when he consoles Aeryn over Crichton's death. Rygel's heartwarming moments always count for double, since he's such a jerk the rest of the time!
The scene in "A Constellation of Doubt" where Chiana is having a breakdown over the dead rat. Doubles as Tear Jerker
At the end of "Relativity," as he fixes up a wounded Rygel (who was briefly dead), Stark says that he saw Zhaan, who he said was at peace and watching over them. Rygel responds by farting helium - something he does in emotional states. Yes, it is possible for a fart joke to be involved in a CMOH.
At the end of "Incubator," Scorpius admires an alien flower which came from the planet where his mother was abducted by the Scarrans, smiling the entire time. It's not unusual for Scorpy to smile, but this one was something different, a genuine sentimental display of emotion, not his usual chilling grin. Though Season 4 added new information about the flowers, this episode clearly intends the meaning to be that Scorpius kept the flower to remember his mother.
In "Into the Lion's Den, Part 2," after Crichton explains the plan to Pilot:
Pilot: We may never see any of you again.
Crichton: Pilot, just be ready to starburst if you don't see us haulin' ass towards you. You give Moya my love.
Pilot: And her love to you... as well as mine.
The euology scene in "Dog With Two Bones", in which Chiana struggles to get through and Rygel steps up:
Chiana: (weeping) Talyn... He uh... he-he was our protector... Mmm... our family...
Rygel: May I say a few words?
Chiana: He uh... he was a lost soul... searching for... uh... (she can't continue, and breaks down as Jool holds her)
Rygel: Talyn was special. A joy to his mother and a credit to his species - both of them. With fondness we lay Talyn - offspring of Moya - to rest in his Sacred Ground.
It's, admittedly, kind of stupid to get attached to a DRD, but you can't help but smile every time John interacts with 1812— particularly when he tells him to "Play nice with the other kids" upon coming back to Moya.
A small moment from "Dream A Little Dream." In the leadup to her trial on Litigara, Zhaan has had a nervous breakdown and is now almost catatonic; when Chiana returns to her cell, she finds Zhaan staring at the wall, chanting quietly... and Rygel holding her hand.
When John takes the notes and the tape recorder he's been narrating into for most of the series and places it on the moon at Tranquility base. After this he will soon close the wormhole that links Earth to the rest of the inhabited galaxy. The notes will help humanity to expand and grow, and he wants humanity to earn them by going back to the moon. He tells this all to his father, and knows he will never see them again, nor will his own son know his grandfather.
The last scene of the Movie has the young child being shown the final battle field of the war, now a beautiful nebula, with a speech letting him know that this is all his now.
The fuzzy relationship between John and Chiana. The scenes that come to mind are:
Chiana leaping into his arms in the season 2 opener after thinking he's been dead.
John trying to keep Chiana from doing something potentially suicidal in "Taking the Stone".
The hug at the end of "A Clockwork Nebari".
Their scene together at the end of "My Three Crichtons."
Tenderly kissing Sikozu in the aftermath of the attack on Katratzi. She initiates the kiss, and Scorpius' initial stunned reaction is one of the few times he comes across as vulnerable. (Wayne Pygram went on to say that he believes it to be Scorpius' first kiss.)
Prior to that, the moment when he silently holds her in the elevator, as the crew believe they're going to perish in the bomb explosion.
In the episode "Exodus from Genesis," Rygel's childish attempt at a self-portrait is ruined when Moya changes course; as he sadly muses on his lost kingdom, Zhaan paints her own portrait of Rygel as she sees him- a majestic figure that bears a close resemblance to the first and most honoured of Rygel's line.
This leads to another heartwarming moment in the same episode, in which Rygel has to negotiate with the Monster of the Week; at first, he's too frightened to approach it- until Zhaan asks "What would Rygel the Great do?" Then, Rygel plucks up his courage, approaches the monster and states:
"I am Rygel, 16th of my lineage, Dominar of the Hynerian Empire. I am at once your equal and your humble petitioner, requesting an audience."
"Goodbye, you big, beautiful, blue bitch."
At the end of "Revenging Angel," Crichton refuses Harvey's attempts to keep him alive with thoughts of revenge, and follows it up by bringing himself back from the dead with thoughts of Aeryn. This is nice enough on its own, but what really makes the scene heartwarming is when Crichton turns to Harvey (who's looking a bit baffled at how things have turned out), pats him on the shoulder, and says, "I do appreciate your help, though."
The ending to "The Way We Weren't." After both Aeryn and Pilot have admitted their guilt and self-loathing over their part in the execution of Moya's first Pilot, Aeryn finally manages to talk Pilot out of his ongoing suicide attempt:
Aeryn: Do you remember when you first came aboard Moya? Velorek stroked your cheek like this to calm you...
(She reaches out and gently strokes Pilot's cheek)
Aeryn: Back then, I couldn't fathom why he would do a thing like that... and now, I couldn't fathom not doing it. We've come a long way since then Pilot.... and we've still got a long way to go: take the journey with me.
(There is a pause, then Pilot extends one of his claws to Aeryn's cheek; she grasps it tenderly.)
And after that, when D'Argo is helping Pilot connect with Moya again. Up until now, Pilot's bonding with Moya was artificial- and actually quite painful to him; this time, D'Argo and the crew connect him naturally with Moya, stating that after years of pain and guilt, he deserves the chance. As the final synapses are linked, Pilot's eyes widen with amazement as he murmurs, "There's no pain... no longer any pain..."
It's worth pointing out that everyone aboard agrees to allowing Pilot to merge naturally, even knowing that it will mean Pilot has less control over Moya for the foreseeable future. When you compare it to the first season, where practically everyone but Crichton is holding Pilot down while tearing off his arm, it's obvious they've come a long way.
In "Look at the Princess, Part III: The Maltese Crichton", [[spoiler: when Aeryn and Crichton kiss at the end, using the chemicals that determine "compatibility". When Aeryn turns around and smiles with that glint of a tear...
What about Crichton "meeting" his daughter with the princess (It Makes Sense in Context)? The one that he'll never get to even see born. If you didn't at least shed Manly Tears for that, you just didn't have a soul.
The moment in "Revenging Angel" when Jool softly kisses Crichton on the forehead as she tends to him.
D'Argo and Chiana's first kiss in "Home on the Remains":
D'Argo: Chiana, you don't have to put on an act for me.
Chiana: D'Argo, I do what I do to survive.
D'Argo: Can't you just let go?
Chiana: I can only let go when I feel safe.
D'Argo: You are safe.
Chiana: Am I?
(D'Argo doesn't say a word in reply. He slowly approaches her and bends down to kiss her softly for a moment. Still not speaking, they look at each other for a while, before he turns and leaves.)
Chiana:(to herself) ...Whoa.
In "Revenging Angel", Jool confessing that her accidental sabotage of D'Argo's ship while she was exploring it was brought on by a desire to understand him a little better.
Jool: I didn't mean to cause any of this-
D'Argo: Well, what did you mean?! I mean - what were you DOING in here?(bows his head and lets out a deep breath)
Jool:(hesitant yet earnest) I know that I can be... difficult. (D'Argo snorts derisively) That no one wants to spend time with me. You're someone who... I like. (D'Argo looks up, surprised, and softens a little) And I know that since the problems with your son and Chiana that you've preferred to be alone. In here - I just thought - if this is so important to you - that maybe... maybe if I learned a little about it - we might have something to talk about.
(A long silence as D'Argo's anger simmers down)
D'Argo:(softly) Thanks for making the effort.
D'Argo and Jool's goodbye kiss in "What Was Lost, Part II".
At the end of PK Wars, when John gives the name of his son, D'Argo Sun-Crichton.
"Season of Death". John and Aeryn are reunited.
John: You're alive!!
"Dog With Two Bones". Cue the swooning of a thousand fangirls.
Aeryn: Do you love Aeryn Sun?
John: [whispers] Beyond hope.
The end of "Through the Looking Glass," where the crew has newfound appreciation for each other and Moya after nearly being killed, after having started the episode making plans to go their separate ways. Pilot announcing that Moya will soon give birth is an added bonus.
John: This is one of the good days, people!
The first shot of Moya in "Promises." The effects, the music and this exchange:
D'Argo: Pilot, Moya looks beautiful. Pilot: She thanks you, Ka D'Argo.
The final scene of "DNA Mad Scientist". D'Argo plays his Shilquen for the first time to Pilot, as a way of apologising for his involvement in cutting off Pilot's arm.
A short while earlier, when Aeryn is recovering from being one of NamTar's test subjects, Crichton tries to make her feel better by arranging food cubes in the shape of a happy face for her.
In "Bad Timing," Crichton has an excellent, complicated plan to save Earth from the Scarrans. He needs the help of Pilot, who can't bring himself to help because of his fear of wormholes. An unlikely character convinces him to do it.
Rygel: You should do it. Pilot: Would you? Rygel: No. But I'm not you.
And then Crichton find out.
Crichton: YOU! Sparky! You selfish, egotistical, self-centered little Dominar! Pilot said it was you that turned him around! Rygel: Do you want to pay me back? Crichton: We'll see how it turns out. I love your scaly green ass no matter what!
Aeryn confesses to Crichton that their baby has been released from stasis and that she's officially pregnant.
Aeryn: It's yours. I just wanted to tell you. Hope it doesn't change anything. Crichton: Umhmm... well it changes everything. WE'RE GONNA HAVE... A BABY! YEAH! (flips a finger at the sky) FRELL YOU! WE ARE GONNA HAVE - A BABYYYYYYYYY!
Crichton teaching Aeryn to slow-dance in the elevator on Katratzi by having her stand on his feet as he led her through the steps. Many Squees were given.